if ((left == null) && (right == null))
{
- if (!(node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder()) && (node.element() != null))
+ if (!(node instanceof SequenceNode
+ && ((SequenceNode) node).isPlaceholder())
+ && (node.element() != null))
{
if (node.element() instanceof SequenceI)
{
// TODO use Character.toLowerCase to avoid creating String objects?
char[] upstream = new String(ds
.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
- .toLowerCase(Locale.ROOT).toCharArray();
+ .toLowerCase(Locale.ROOT).toCharArray();
char[] downstream = new String(
ds.getSequence(s_end - 1, s_end + dstream_ds))
- .toLowerCase(Locale.ROOT).toCharArray();
+ .toLowerCase(Locale.ROOT).toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
+ coreseq.length];
*/
final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
.findAnnotations(seq, dsann.getCalcId(), dsann.label);
- boolean found=false;
+ boolean found = false;
if (matchedAlignmentAnnotations != null)
{
- for (AlignmentAnnotation matched:matchedAlignmentAnnotations)
+ for (AlignmentAnnotation matched : matchedAlignmentAnnotations)
{
if (dsann.description.equals(matched.description))
{
- found=true;
+ found = true;
break;
}
}
}
- if (!found) {
+ if (!found)
+ {
result.add(dsann);
if (labelForCalcId != null)
{
/**
* Adds annotations to the top of the alignment annotations, in the same order
- * as their related sequences. If you already have an annotation and want to add it to a sequence in an alignment use {@code addReferenceAnnotationTo}
+ * as their related sequences. If you already have an annotation and want to
+ * add it to a sequence in an alignment use {@code addReferenceAnnotationTo}
*
* @param annotations
* the annotations to add
{
for (AlignmentAnnotation ann : annotations.get(seq))
{
- addReferenceAnnotationTo(alignment, seq,ann,selectionGroup);
+ addReferenceAnnotationTo(alignment, seq, ann, selectionGroup);
}
}
}
+
/**
- * Make a copy of a reference annotation {@code ann} and add it to an alignment sequence {@code seq} in {@code alignment}, optionally limited to the extent of {@code selectionGroup}
+ * Make a copy of a reference annotation {@code ann} and add it to an
+ * alignment sequence {@code seq} in {@code alignment}, optionally limited to
+ * the extent of {@code selectionGroup}
+ *
* @param alignment
* @param seq
* @param ann
- * @param selectionGroup - may be null
+ * @param selectionGroup
+ * - may be null
* @return annotation added to {@code seq and {@code alignment}
*/
- public static AlignmentAnnotation addReferenceAnnotationTo(final AlignmentI alignment, final SequenceI seq,final AlignmentAnnotation ann,final SequenceGroup selectionGroup)
+ public static AlignmentAnnotation addReferenceAnnotationTo(
+ final AlignmentI alignment, final SequenceI seq,
+ final AlignmentAnnotation ann, final SequenceGroup selectionGroup)
{
- AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
- int startRes = 0;
- int endRes = ann.annotations.length;
- if (selectionGroup != null)
- {
- startRes = -1+Math.min(seq.getEnd(), Math.max(seq.getStart(),seq.findPosition(selectionGroup.getStartRes())));
- endRes = -1+Math.min(seq.getEnd(),seq.findPosition(selectionGroup.getEndRes()));
-
- }
- copyAnn.restrict(startRes, endRes + 0);
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ if (selectionGroup != null)
+ {
+ startRes = -1 + Math.min(seq.getEnd(), Math.max(seq.getStart(),
+ seq.findPosition(selectionGroup.getStartRes())));
+ endRes = -1 + Math.min(seq.getEnd(),
+ seq.findPosition(selectionGroup.getEndRes()));
- /*
- * Add to the sequence (sets copyAnn.datasetSequence), unless the
- * original annotation is already on the sequence.
- */
- if (!seq.hasAnnotation(ann))
- {
- ContactMatrixI cm = seq.getDatasetSequence()
- .getContactMatrixFor(ann);
- if (cm != null)
- {
- seq.addContactListFor(copyAnn, cm);
- }
- seq.addAlignmentAnnotation(copyAnn);
- }
- // adjust for gaps
- copyAnn.adjustForAlignment();
- // add to the alignment and set visible
- alignment.addAnnotation(copyAnn);
- copyAnn.visible = true;
-
- return copyAnn;
+ }
+ copyAnn.restrict(startRes, endRes + 0);
+
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ ContactMatrixI cm = seq.getDatasetSequence().getContactMatrixFor(ann);
+ if (cm != null)
+ {
+ seq.addContactListFor(copyAnn, cm);
+ }
+ seq.addAlignmentAnnotation(copyAnn);
+ }
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ alignment.addAnnotation(copyAnn);
+ copyAnn.visible = true;
+
+ return copyAnn;
}
/**
return showAutocalcAbove ? 1 : -1;
}
int computedOrder = compareSequences(o1, o2);
- if (computedOrder==0) {
+ if (computedOrder == 0)
+ {
computedOrder = compareLabels(o1, o2);
}
- if (computedOrder==0)
+ if (computedOrder == 0)
{
- computedOrder = compareDescriptions(o1,o2);
+ computedOrder = compareDescriptions(o1, o2);
}
return computedOrder;
}
}
String label1 = o1.label;
String label2 = o2.label;
- return compareString(label1,label2);
+ return compareString(label1, label2);
}
/**
- * Non-case-sensitive comparison of annotation descriptions. Returns zero if either
- * argument is null.
+ * Non-case-sensitive comparison of annotation descriptions. Returns zero if
+ * either argument is null.
*
* @param o1
* @param o2
* @return
*/
- private int compareDescriptions(AlignmentAnnotation o1, AlignmentAnnotation o2)
+ private int compareDescriptions(AlignmentAnnotation o1,
+ AlignmentAnnotation o2)
{
if (o1 == null || o2 == null)
{
}
String label1 = o1.description;
String label2 = o2.description;
- return compareString(label1,label2);
+ return compareString(label1, label2);
}
+
private int compareString(String label1, String label2)
{
if (label1 == null && label2 == null)
{
distances.setValue(i, i, 0);
ContactListI jth = cm.getContactList(j);
- if (jth==null)
+ if (jth == null)
{
break;
}
public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
- this(seqs, treefile.getTree(), treefile.HasDistances(),
+ this(seqs, treefile.getTree(), treefile.HasDistances(),
treefile.HasBootstrap(), treefile.HasRootDistance());
seqData = odata;
*/
public TreeModel(TreeBuilder tree)
{
- this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
+ this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
while (i < leaves.size())
{
// TODO - decide if we get rid of the polymorphism here ?
- j = (SequenceNode)leaves.elementAt(i++);
+ j = (SequenceNode) leaves.elementAt(i++);
realnam = j.getName();
nam = null;
*
* @return Vector of leaf nodes on binary tree
*/
- Vector<BinaryNode> findLeaves(BinaryNode nd,
- Vector<BinaryNode> leaves)
+ Vector<BinaryNode> findLeaves(BinaryNode nd, Vector<BinaryNode> leaves)
{
if (nd == null)
{
SearchResultsI getSearchResults();
/**
- * Retrieve a ContactListI corresponding to column in an annotation row in an alignment.
- * @param _aa - annotation with associated matrix data
- * @param column - column in alignment where _aa is associated
+ * Retrieve a ContactListI corresponding to column in an annotation row in an
+ * alignment.
+ *
+ * @param _aa
+ * - annotation with associated matrix data
+ * @param column
+ * - column in alignment where _aa is associated
*/
ContactListI getContactList(AlignmentAnnotation _aa, int column);
{
BinaryNode lf = leaves.elementAt(i);
- if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
+ if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
{
has_placeholders = true;
}
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node instanceof SequenceNode && ((SequenceNode) node).isPlaceholder())
- ? (PLACEHOLDER + node.getName())
- : node.getName();
+ String name = (markPlaceholders && node instanceof SequenceNode
+ && ((SequenceNode) node).isPlaceholder())
+ ? (PLACEHOLDER + node.getName())
+ : node.getName();
FontMetrics fm = g.getFontMetrics(font);
int charWidth = fm.stringWidth(name) + 3;
int charHeight = fm.getHeight();
}
else
{
- pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width,
- offx, offy);
+ pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx,
+ offy);
pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width,
offx, offy);
}
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
- (protocol.equalsIgnoreCase("http")
- && (httpUser != null
- && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
{
ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
- if (cm==null && _aa.groupRef!=null)
+ if (cm == null && _aa.groupRef != null)
{
cm = _aa.groupRef.getContactMatrixFor(_aa);
}
- if (cm==null && _aa.sequenceRef!=null)
+ if (cm == null && _aa.sequenceRef != null)
{
cm = _aa.sequenceRef.getContactMatrixFor(_aa);
- if (cm==null)
+ if (cm == null)
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
&& spos <= 1 + _aa.sequenceRef.getEnd())
{
cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
- spos-_aa.sequenceRef.getStart());
+ spos - _aa.sequenceRef.getStart());
}
}
}
: annotations[index + offset].displayCharacter == null
|| annotations[index
+ offset].displayCharacter
- .length() == 0
- ? annotations[index
- + offset].secondaryStructure
- : annotations[index
- + offset].displayCharacter
- .charAt(0));
+ .length() == 0
+ ? annotations[index
+ + offset].secondaryStructure
+ : annotations[index
+ + offset].displayCharacter
+ .charAt(0));
}
@Override
/** DOCUMENT ME!! */
public Color color = Color.black;
- /** if true, node is created to simulate polytomy between parent and its 3 or more children */
+ /**
+ * if true, node is created to simulate polytomy between parent and its 3 or
+ * more children
+ */
public boolean dummy = false;
/**
}
/**
- * add a series of start,end (inclusive) ranges to the column selection
- * @param rng [start_0, end_0, start_1, end_1, ... ]
- * @param baseOne - when true, ranges are base 1 and will be mapped to base 0
+ * add a series of start,end (inclusive) ranges to the column selection
+ *
+ * @param rng
+ * [start_0, end_0, start_1, end_1, ... ]
+ * @param baseOne
+ * - when true, ranges are base 1 and will be mapped to base 0
*/
- public void addRangeOfElements(int[] rng,boolean baseOne)
+ public void addRangeOfElements(int[] rng, boolean baseOne)
{
- int base=baseOne ? -1 : 0;
+ int base = baseOne ? -1 : 0;
for (int c = 0; c < rng.length; c += 2)
{
for (int p = rng[c]; p <= rng[c + 1]; p++)
{
- selection.add(base+p);
+ selection.add(base + p);
}
}
-
+
}
+
/**
* clears column selection
*/
int cpos = ann_row.sequenceRef.findPosition(column) - 1;
ContactListI clist = ann_row.sequenceRef
.getContactListFor(ann_row, cpos);
- for (int row = column + 8,
- rowEnd = clist.getContactHeight(); row < rowEnd; row++)
+ for (int row = column + 8, rowEnd = clist
+ .getContactHeight(); row < rowEnd; row++)
{
if (filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
*/
ContactRange getRangeFor(int from_column, int to_column);
- default Color getColourForGroup() {
+ default Color getColourForGroup()
+ {
return null;
}
}
}
return cr;
}
+
@Override
public int[] getMappedPositionsFor(int cStart, int cEnd)
{
- return clist.getMappedPositionsFor(cStart, cEnd);
+ return clist.getMappedPositionsFor(cStart, cEnd);
}
+
@Override
public Color getColourForGroup()
{
*/
double getContactAt(int column);
-
/**
- * Return positions in local reference corresponding to cStart and cEnd in matrix data. Positions are base 1 column indices for sequence associated matrices.
+ * Return positions in local reference corresponding to cStart and cEnd in
+ * matrix data. Positions are base 1 column indices for sequence associated
+ * matrices.
+ *
* @param cStart
* @param cEnd
* @return int[] { start, end (inclusive) for each contiguous segment}
*/
- default int[] getMappedPositionsFor(int cStart, int cEnd) {
- return new int[] { cStart, cEnd};
+ default int[] getMappedPositionsFor(int cStart, int cEnd)
+ {
+ return new int[] { cStart, cEnd };
}
- default Color getColourForGroup() {
+ default Color getColourForGroup()
+ {
return null;
}
}
if (cm instanceof MappableContactMatrixI)
{
- if (_aa.sequenceRef!=null)
+ if (_aa.sequenceRef != null)
{
- return ((MappableContactMatrixI)cm).getMappableContactList(_aa.sequenceRef, column);
+ return ((MappableContactMatrixI) cm)
+ .getMappableContactList(_aa.sequenceRef, column);
}
}
// TODO: could resolve sequence position to column position here
{
return "Contact Matrix";
}
+
GroupSet grps = new GroupSet();
+
@Override
public GroupSetI getGroupSet()
{
return grps;
}
+
@Override
public void setGroupSet(GroupSet makeGroups)
{
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
- for (int c=0;c<cm.getWidth();c++)
+ for (int c = 0; c < cm.getWidth(); c++)
{
- ContactListI cl=cm.getContactList(c);
- if (cl!=null) {
- for (int h=0;h<=cl.getContactHeight();h++)
+ ContactListI cl = cm.getContactList(c);
+ if (cl != null)
{
- if (sb.length()>0) {
- sb.append('\t');
+ for (int h = 0; h <= cl.getContactHeight(); h++)
+ {
+ if (sb.length() > 0)
+ {
+ sb.append('\t');
+ }
+ sb.append(cl.getContactAt(h));
}
- sb.append(cl.getContactAt(h));
- }
}
}
return sb.toString();
int rows)
{
float[][] vals = new float[cols][rows];
- StringTokenizer tabsep = new StringTokenizer(values,""+'\t');
- int c=0,r=0;
-
+ StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+ int c = 0, r = 0;
+
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
- vals[c][r++]=(float) elem;
- if (r>=vals[c].length)
+ vals[c][r++] = (float) elem;
+ if (r >= vals[c].length)
{
- r=0;
+ r = 0;
c++;
}
- if (c>=vals.length)
+ if (c >= vals.length)
{
-
+
break;
}
}
if (tabsep.hasMoreElements())
{
- Console.warn("Ignoring additional elements for Float string to contact matrix parsing.");
+ Console.warn(
+ "Ignoring additional elements for Float string to contact matrix parsing.");
}
-
+
return vals;
}
}
String getAnnotLabel();
/**
- * string indicating how the contactMatrix should be rendered - stored in calcId
- * @return
+ * string indicating how the contactMatrix should be rendered - stored in
+ * calcId
+ *
+ * @return
*/
String getType();
int getWidth();
+
int getHeight();
-
+
public GroupSetI getGroupSet();
-
+
/// proxy methods to simplify use of the interface
/// Mappable contact matrices can override these to perform mapping
-
+
default public boolean hasGroupSet()
{
- return getGroupSet()!=null;
+ return getGroupSet() != null;
}
- default boolean hasGroups() {
+ default boolean hasGroups()
+ {
return hasGroupSet() && getGroupSet().hasGroups();
}
-
- default BitSet getGroupsFor(int column) {
+ default BitSet getGroupsFor(int column)
+ {
if (!hasGroupSet())
{
- BitSet colbitset = new BitSet();
- colbitset.set(column);
- return colbitset;
+ BitSet colbitset = new BitSet();
+ colbitset.set(column);
+ return colbitset;
}
return getGroupSet().getGroupsFor(column);
}
- default List<BitSet> getGroups() {
+ default List<BitSet> getGroups()
+ {
if (!hasGroupSet())
{
- return Arrays.asList();
- }
+ return Arrays.asList();
+ }
return getGroupSet().getGroups();
}
- default boolean hasTree() {
+ default boolean hasTree()
+ {
return hasGroupSet() ? getGroupSet().hasTree() : false;
}
/**
* Newick representation of clustered matrix
+ *
* @return null unless hasTree is true
*/
- default String getNewick() {
- return hasGroupSet() ? getGroupSet().getNewick(): null;
+ default String getNewick()
+ {
+ return hasGroupSet() ? getGroupSet().getNewick() : null;
}
- default String getTreeMethod() {
- return hasGroupSet() ? getGroupSet().getTreeMethod() :null;
+ default String getTreeMethod()
+ {
+ return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
}
- default boolean hasCutHeight() {
+ default boolean hasCutHeight()
+ {
return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
}
- default double getCutHeight() {
- return hasGroupSet() ? getGroupSet().getCutHeight():0;
+ default double getCutHeight()
+ {
+ return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
}
default void updateGroups(List<BitSet> colGroups)
package jalview.datamodel;
-
/**
* bean for max/min positions for a given range
*
* @param maxPos
* @param max
*/
- public void update(int from_column, int to_column, int minPos,
- double min, int maxPos, double max, double mean)
+ public void update(int from_column, int to_column, int minPos, double min,
+ int maxPos, double max, double mean)
{
this.from_column = from_column;
this.to_column = to_column;
public GroupSet(GroupSet grps)
{
- abs=grps.abs;
- colorMap=new HashMap<BitSet, Color>(grps.colorMap);
- groups=new ArrayList<BitSet>(grps.groups);
- newick=grps.newick;
- thresh=grps.thresh;
- treeType=grps.treeType;
+ abs = grps.abs;
+ colorMap = new HashMap<BitSet, Color>(grps.colorMap);
+ groups = new ArrayList<BitSet>(grps.groups);
+ newick = grps.newick;
+ thresh = grps.thresh;
+ treeType = grps.treeType;
}
public GroupSet()
thresh = thresh2;
groups = groups2;
treeType = treeType2;
- newick=newick2;
+ newick = newick2;
}
@Override
return newick != null && newick.length() > 0;
}
- boolean abs=false;
+ boolean abs = false;
- double thresh=0;
+ double thresh = 0;
String treeType = null;
}
groups.add(gpset);
}
- GroupSet grps = new GroupSet(abs,thresh,groups,treeType, newick);
+ GroupSet grps = new GroupSet(abs, thresh, groups, treeType, newick);
return grps;
}
* @author jprocter
*
*/
-public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceContactMatrix> implements ContactMatrixI
+public class SeqDistanceContactMatrix
+ extends MappableContactMatrix<SeqDistanceContactMatrix>
+ implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
private int width = 0;
public SeqDistanceContactMatrix(int width)
}
});
}
+
@Override
public String getAnnotDescr()
{
{
return width;
}
+
@Override
protected double getElementAt(int _column, int i)
{
- return Math.abs(_column-i);
+ return Math.abs(_column - i);
}
@Override
protected SeqDistanceContactMatrix newMappableContactMatrix(
SequenceI newRefSeq, MapList newFromMapList)
{
-
+
return new SeqDistanceContactMatrix(width);
}
}
AlignmentAnnotation aa = cmholder.addContactList(cm);
Annotation _aa[] = new Annotation[getLength()];
-
+
for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
{
;
}
aa.annotations = _aa;
aa.setSequenceRef(this);
- if (cm instanceof MappableContactMatrix && !((MappableContactMatrix) cm).hasReferenceSeq())
+ if (cm instanceof MappableContactMatrix
+ && !((MappableContactMatrix) cm).hasReferenceSeq())
{
((MappableContactMatrix) cm).setRefSeq(this);
}
super();
}
- public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent, String name,
- double dist, int bootstrap, boolean dummy)
+ public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap, boolean dummy)
{
super(val, parent, name, dist, bootstrap, dummy);
}
- public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent, String name,
- double dist, int bootstrap)
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap)
{
super(element, parent, name, dist, bootstrap);
}
- public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent, String name,
- double dist)
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist)
{
super(element, parent, name, dist);
}
name = string;
}
- public AnnotationRowBuilder(String name, float min, float max, StructureImportSettings.TFType tft)
+ public AnnotationRowBuilder(String name, float min, float max,
+ StructureImportSettings.TFType tft)
{
this(name, min, max);
setTFType(tft);
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
- boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
- false);
+ boolean showHiddenRegions = Cache
+ .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
openOverviewPanel(showHiddenRegions);
}
return alignPanel.overviewPanel;
}
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
+ final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
+ showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
- true, true);
+ Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
+ frame.getHeight(), true, true);
frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- final AlignmentPanel thePanel = this.alignPanel;
+ final AlignmentPanel thePanel = this.alignPanel;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
alignPanel.setOverviewPanel(overview);
alignPanel.setOverviewTitle(this);
-
+
return overview;
}
return showNewickTree(nf, treeTitle, null, w, h, x, y);
}
-
/**
* Add a treeviewer for the tree extracted from a Newick file object to the
* current alignment view
return tp;
}
-
public void showContactMapTree(AlignmentAnnotation aa,
PAEContactMatrix cm)
{
int x = 4, y = 5;
int w = 400, h = 500;
-
+
try
{
NewickFile fin = new NewickFile(
String title = "PAE Matrix Tree for "
+ cm.getReferenceSeq().getDisplayId(false);
- showColumnWiseTree(fin, aa, title, w,h, x,y);
+ showColumnWiseTree(fin, aa, title, w, h, x, y);
} catch (Throwable xx)
{
Console.error("Unexpected exception showing tree for contact matrix",
xx);
}
}
- public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle,
- int w, int h, int x, int y)
+
+ public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
+ String treeTitle, int w, int h, int x, int y)
{
- try
+ try
+ {
+ nf.parse();
+ if (nf.getTree() == null)
{
- nf.parse();
- if (nf.getTree() == null)
- {
- return null;
- }
- TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
-
- tp.setSize(w, h);
+ return null;
+ }
+ TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
- if (x > 0 && y > 0)
- {
- tp.setLocation(x, y);
- }
+ tp.setSize(w, h);
- Desktop.addInternalFrame(tp, title, w, h);
- return tp;
- } catch (Throwable xx)
+ if (x > 0 && y > 0)
{
- Console.error("Unexpected exception showing tree for contact matrix",
- xx);
+ tp.setLocation(x, y);
}
- return null;
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ return tp;
+ } catch (Throwable xx)
+ {
+ Console.error("Unexpected exception showing tree for contact matrix",
+ xx);
+ }
+ return null;
}
-
+
private boolean buildingMenu = false;
/**
* to add view name "Original" if necessary
*/
alignPanel.setOverviewTitle(this);
-
+
/*
* switch panels and set Overview title (if there is one
* because it was opened automatically)
viewStyle.setFontName(font.getName());
viewStyle.setFontStyle(font.getStyle());
viewStyle.setFontSize(font.getSize());
-
+
validCharWidth = true;
}
// set idCanvas bufferedImage to null
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
-
- // update the flag controlling whether the grid is too small to render the font
+
+ // update the flag controlling whether the grid is too small to render the
+ // font
av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
scalePanelHolder.setPreferredSize(
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
- if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
+ if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
&& PAEContactMatrix.PAEMATRIX
.equals(aa[selectedRow].getCalcId()))
{
final PAEContactMatrix cm = (PAEContactMatrix) av
.getContactMatrix(aa[selectedRow]);
- if (cm!=null && cm.hasTree())
+ if (cm != null && cm.hasTree())
{
item = new JMenuItem("Show Tree for Matrix");
item.addActionListener(new ActionListener()
public void actionPerformed(ActionEvent e)
{
- ap.alignFrame.showContactMapTree(aa[selectedRow],cm);
+ ap.alignFrame.showContactMapTree(aa[selectedRow], cm);
}
});
}
olY = y;
// look ahead to next annotation
- for (nexAA=i+1; nexAA<aa.length && !aa[nexAA].visible; nexAA++)
+ for (nexAA = i + 1; nexAA < aa.length
+ && !aa[nexAA].visible; nexAA++)
;
y += aa[i].height;
if (clip)
{
if (vertBar)
{
- g.drawLine(width-3, y + offset-fontHeight, width-3, (int)(y - 1.5*aa[i].height-offset-fontHeight));
+ g.drawLine(width - 3, y + offset - fontHeight, width - 3,
+ (int) (y - 1.5 * aa[i].height - offset - fontHeight));
// g.drawLine(20, y + offset, x - 20, y + offset);
}
}
else
{
- // no row (or row that can be adjusted) was pressed. Simulate a ruler click
+ // no row (or row that can be adjusted) was pressed. Simulate a ruler
+ // click
ap.getScalePanel().mousePressed(evt);
}
}
}
c--;
}
- c = to;
- while (c < forCurrentX.getContactHeight())
+ c = to;
+ while (c < forCurrentX.getContactHeight())
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
{
- cval = forCurrentX.getContactAt(c);
- if (// cr.getMin() <= cval &&
- cval <= thresh)
- {
- int[] cols = forCurrentX.getMappedPositionsFor(c, c);
- if (cols != null)
- {
- av.getColumnSelection().addRangeOfElements(cols, true);
- }
- }
- else
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
{
- break;
+ av.getColumnSelection().addRangeOfElements(cols, true);
}
- c++;
-
}
+ else
+ {
+ break;
+ }
+ c++;
+
}
+ }
}
}
ap.paintAlignment(false, false);
av.sendSelection();
return true;
}
+
/**
* Construct and display a context menu at the right-click position
*
}
if (rowIndex[0] != toRowIndex[0])
{
- jalview.bin.Console.trace("Drag went to another row. needs to be clipped");
+ jalview.bin.Console
+ .trace("Drag went to another row. needs to be clipped");
}
// rectangular selection on matrix style annotation
for (int pair = 0; pair < mappedPos.length; pair += 2)
{
for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
-// {
-// if (cma.sequenceRef != null)
-// {
-// int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
-// av.getColumnSelection().addElement(col);
-// }
-// else
- {
- av.getColumnSelection().addElement(c);
- }
+ // {
+ // if (cma.sequenceRef != null)
+ // {
+ // int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+ // av.getColumnSelection().addElement(col);
+ // }
+ // else
+ {
+ av.getColumnSelection().addElement(c);
+ }
}
}
// and again for most recent corner of drag
for (int pair = 0; pair < mappedPos.length; pair += 2)
{
jalview.bin.Console.trace("Marking " + fr + " to " + to
- + " mapping to sequence positions " + mappedPos[pair] + " to "
- + mappedPos[pair+1]);
+ + " mapping to sequence positions " + mappedPos[pair]
+ + " to " + mappedPos[pair + 1]);
for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
{
-// if (cma.sequenceRef != null)
-// {
-// int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
-// av.getColumnSelection().addElement(col);
-// }
-// else
+ // if (cma.sequenceRef != null)
+ // {
+ // int col =
+ // cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+ // av.getColumnSelection().addElement(col);
+ // }
+ // else
{
av.getColumnSelection().addElement(c);
}
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
-
+
int col = ann.sequenceRef.findPosition(column);
int[][] highlightPos;
int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd);
// TODO - write tests and fix AlignFrame.paste() which doesn't track if
// clipboard has come from a different alignment window than the one where
// paste has been called! JAL-4151
-
+
if (Desktop.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
}
Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_HEIGHT);
- } else {
- try
+ }
+ else
{
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable contents = c.getContents(this);
-
- if (contents != null)
+ try
{
- String file = (String) contents
- .getTransferData(DataFlavor.stringFlavor);
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
- FileFormatI format = new IdentifyFile().identify(file,
- DataSourceType.PASTE);
+ if (contents != null)
+ {
+ String file = (String) contents
+ .getTransferData(DataFlavor.stringFlavor);
- new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+ FileFormatI format = new IdentifyFile().identify(file,
+ DataSourceType.PASTE);
+ new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+
+ }
+ } catch (Exception ex)
+ {
+ System.out.println(
+ "Unable to paste alignment from system clipboard:\n" + ex);
}
- } catch (Exception ex)
- {
- System.out.println(
- "Unable to paste alignment from system clipboard:\n" + ex);
- }
}
}
OVERVIEW_DEFAULT_GAP);
Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
OVERVIEW_DEFAULT_HIDDEN);
- Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE;
-
+ Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE
+ : OVERVIEW_DEFAULT_RESIDUE;
+
cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol);
setSize(od.getWidth(), od.getHeight());
qd.showDialogOnTopAsync(
new StringBuilder(
MessageManager.getString("label.quit_jalview"))
- .append("\n").append(messageString).toString(),
+ .append("\n").append(messageString)
+ .toString(),
MessageManager.getString("action.quit"),
JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, null,
new Object[]
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String fileName = chooser.getSelectedFile().getPath();
- try {
+ try
+ {
PAEContactMatrix.validateContactMatrixFile(fileName);
} catch (Exception thr)
{
JvOptionPane.showInternalMessageDialog(this, MessageManager
.formatMessage("label.couldnt_load_file", new Object[]
- { fileName})+"<br>"+thr.getLocalizedMessage(),
+ { fileName }) + "<br>" + thr.getLocalizedMessage(),
MessageManager.getString("label.error_loading_file"),
JvOptionPane.WARNING_MESSAGE);
- Console.error("Couldn't import "+fileName+" as a PAE matrix",thr);
+ Console.error("Couldn't import " + fileName + " as a PAE matrix",
+ thr);
return;
}
localPdbPaeMatrixFileName = fileName;
btn_newView.setEnabled(false);
btn_cancel.setEnabled(false);
actionsPanel.setEnabled(false);
-
- final String progress=MessageManager.getString("label.working_ellipsis");
+
+ final String progress = MessageManager
+ .getString("label.working_ellipsis");
setProgressBar(progress, progress.hashCode());
Runnable viewStruc = new Runnable()
{
{
BinaryNode lf = leaves.elementAt(i);
- if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
+ if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
{
has_placeholders = true;
}
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder())))
- ? (PLACEHOLDER + node.getName())
- : node.getName();
+ String name = (markPlaceholders && ((node instanceof SequenceNode
+ && ((SequenceNode) node).isPlaceholder())))
+ ? (PLACEHOLDER + node.getName())
+ : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
int ystart = (node.left() == null ? 0
: (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
int yend = (node.right() == null ? 0
- : (int) (((BinaryNode) node.right()).ycount * chunk))
- + offy;
+ : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
else
{
Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
- if (tp.isColumnWise()) {
- markColumnsFor(getAssociatedPanels(), leaves, Color.red);
- } else {
- for (int i = 0; i < leaves.size(); i++)
+ if (tp.isColumnWise())
{
- SequenceI seq = (SequenceI) leaves.elementAt(i).element();
- treeSelectionChanged(seq);
+ markColumnsFor(getAssociatedPanels(), leaves, Color.red);
}
+ else
+ {
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+ treeSelectionChanged(seq);
+ }
}
av.sendSelection();
}
{
AlignmentPanel[] aps = getAssociatedPanels();
List<BitSet> colGroups = new ArrayList<>();
- Map<BitSet,Color> colors=new HashMap();
+ Map<BitSet, Color> colors = new HashMap();
for (int i = 0; i < groups.size(); i++)
{
Color col = new Color((int) (Math.random() * 255),
setColor(groups.get(i), col.brighter());
Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
- if (!tp.isColumnWise()) {
+ if (!tp.isColumnWise())
+ {
createSeqGroupFor(aps, l, col);
- } else {
- BitSet gp=createColumnGroupFor(l,col);
+ }
+ else
+ {
+ BitSet gp = createColumnGroupFor(l, col);
colGroups.add(gp);
colors.put(gp, col);
if (tp.isColumnWise())
{
AlignmentAnnotation aa = tp.getAssocAnnotation();
- if (aa!=null) {
+ if (aa != null)
+ {
ContactMatrixI cm = av.getContactMatrix(aa);
- if (cm!=null)
+ if (cm != null)
{
cm.updateGroups(colGroups);
- for (BitSet gp:colors.keySet())
+ for (BitSet gp : colors.keySet())
{
cm.setColorForGroup(gp, colors.get(gp));
}
}
// stash colors in linked annotation row.
// doesn't work yet. TESTS!
- int sstart=aa.sequenceRef!=null ? aa.sequenceRef.getStart()-1 : 0;
+ int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+ : 0;
Annotation ae;
Color gpcol = null;
- int[] seqpos=null;
+ int[] seqpos = null;
for (BitSet gp : colors.keySet())
{
gpcol = colors.get(gp);
- for (int p = gp.nextSetBit(0); p >= 0 && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+ for (int p = gp.nextSetBit(0); p >= 0
+ && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
{
if (cm instanceof MappableContactMatrixI)
{
MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
- seqpos = mcm.getMappedPositionsFor(aa.sequenceRef,p);
- if (seqpos==null)
+ seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+ if (seqpos == null)
{
// no mapping for this column.
continue;
}
// TODO: handle ranges...
ae = aa.getAnnotationForPosition(seqpos[0]);
- } else {
- ae = aa.getAnnotationForPosition(p+sstart);
+ }
+ else
+ {
+ ae = aa.getAnnotationForPosition(p + sstart);
}
if (ae != null)
{
{
return false;
}
- if (av==null||av.getAlignment()==null)
+ if (av == null || av.getAlignment() == null)
{
// alignment is closed
return false;
}
ColumnSelection cs = av.getColumnSelection();
-
+
HiddenColumns hc = av.getAlignment().getHiddenColumns();
int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
: colm;
if (!av.hasHiddenColumns())
{
- return cs.contains(offp-1);
+ return cs.contains(offp - 1);
}
- if (hc.isVisible(offp-1))
+ if (hc.isVisible(offp - 1))
{
- return cs.contains(offp-1);
-// return cs.contains(hc.absoluteToVisibleColumn(offp));
+ return cs.contains(offp - 1);
+ // return cs.contains(hc.absoluteToVisibleColumn(offp));
}
return false;
}
-
- private BitSet createColumnGroupFor(Vector<BinaryNode> l,
- Color col)
+
+ private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
{
- BitSet gp=new BitSet();
- for (BinaryNode bn:l)
+ BitSet gp = new BitSet();
+ for (BinaryNode bn : l)
{
- int colm=-1;
- if (bn.element()!=null && bn.element()instanceof Integer)
- { colm = (Integer)bn.element();
- } else {
- // parse out from nodename
- try {
- colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
- } catch (Exception e)
+ int colm = -1;
+ if (bn.element() != null && bn.element() instanceof Integer)
{
- continue;
+ colm = (Integer) bn.element();
}
+ else
+ {
+ // parse out from nodename
+ try
+ {
+ colm = Integer.parseInt(
+ bn.getName().substring(bn.getName().indexOf("c") + 1));
+ } catch (Exception e)
+ {
+ continue;
+ }
}
gp.set(colm);
}
Color col)
{
SequenceI rseq = tp.assocAnnotation.sequenceRef;
-
+
if (av == null || av.getAlignment() == null)
{
// alignment is closed
continue;
}
// TODO - sort indices for faster lookup
-
+
ColumnSelection cs = av.getColumnSelection();
HiddenColumns hc = av.getAlignment().getHiddenColumns();
ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
if (cm instanceof MappableContactMatrixI)
{
mcm = (MappableContactMatrixI) cm;
- int[] seqpos = mcm.getMappedPositionsFor(tp.assocAnnotation.sequenceRef,colm);
- if (seqpos==null)
+ int[] seqpos = mcm.getMappedPositionsFor(
+ tp.assocAnnotation.sequenceRef, colm);
+ if (seqpos == null)
{
// no mapping for this column.
continue;
}
// TODO: handle ranges...
- offp=seqpos[0];
+ offp = seqpos[0];
}
else
{
AlignmentAnnotation aa, String title)
{
super();
- columnWise=true;
+ columnWise = true;
assocAnnotation = aa;
this.setFrameIcon(null);
this.treeTitle = title;
initTreePanel(alignPanel, null, null, fin, null);
}
-
- boolean columnWise=false;
- AlignmentAnnotation assocAnnotation=null;
+
+ boolean columnWise = false;
+
+ AlignmentAnnotation assocAnnotation = null;
+
public boolean isColumnWise()
{
return columnWise;
}
- public AlignmentAnnotation getAssocAnnotation() {
+
+ public AlignmentAnnotation getAssocAnnotation()
+ {
return assocAnnotation;
}
true, false);
((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
.getComponent(0))
- .setText(ensureHtmlTagged(
- txt + getHtmlFragment(text, false, true)));
+ .setText(ensureHtmlTagged(
+ txt + getHtmlFragment(text, false, true)));
}
else
{
}
String encoding = _conn.getContentEncoding();
String contentType = _conn.getContentType();
- boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType) || contentType.endsWith("gzip")
- || "gzip".equals(encoding);
+ boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
+ || contentType.endsWith("gzip") || "gzip".equals(encoding);
Exception e = null;
InputStream inputStream = _conn.getInputStream();
if (isgzipped)
{
try
{
- distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
+ distance = (Double.valueOf(ndist.stringMatched(1)))
+ .floatValue();
HasDistances = true;
nodehasdistance = true;
} catch (Exception e)
{
if (root.isDummy())
{
- _print(tf, root.right());
- _print(tf, root.left());
+ _print(tf, root.right());
+ _print(tf, root.left());
}
else
{
tf.append("(");
- _print(tf, root.right());
+ _print(tf, root.right());
if (root.left() != null)
{
tf.append(",");
}
- _print(tf, root.left());
+ _print(tf, root.left());
tf.append(")" + printRootField(root));
}
}
{
if (c.isDummy())
{
- _print(tf, c.left());
+ _print(tf, c.left());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, c.right());
+ _print(tf, c.right());
}
else
{
tf.append("(");
- _print(tf, c.right());
+ _print(tf, c.right());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, c.left());
+ _print(tf, c.left());
tf.append(")" + printNodeField(c));
}
}
{
protected static final String CONTACT_PREDICTION = "CONTACT_PREDICTION";
- public PContactPredictionFile(String inFile, DataSourceType fileSourceType)
- throws IOException
+ public PContactPredictionFile(String inFile,
+ DataSourceType fileSourceType) throws IOException
{
super(inFile, fileSourceType);
if (cm == null)
{
- cm = new ContactMatrix(true) {
+ cm = new ContactMatrix(true)
+ {
@Override
public String getType()
{
return CONTACT_PREDICTION;
}
+
@Override
public int getHeight()
{
// TODO Auto-generated method stub
- // return maximum contact height
+ // return maximum contact height
return 0;
- }@Override
+ }
+
+ @Override
public int getWidth()
{
// TODO Auto-generated method stub
} catch (Exception x)
{
error = true;
- errormessage = "Couldn't process line: "
- + x.getLocalizedMessage() + "\n" + line;
+ errormessage = "Couldn't process line: " + x.getLocalizedMessage()
+ + "\n" + line;
return;
}
cm.addContact(left, right, (float) strength);
}
}
// TODO COMPLETE
- throw(new Error("Not Implemented yet."));
+ throw (new Error("Not Implemented yet."));
}
@Override
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
- throw new IOException(MessageManager
- .getString("exception.stockholm_invalid_format") +" ("+r+")");
+ throw new IOException(
+ MessageManager.getString("exception.stockholm_invalid_format")
+ + " (" + r + ")");
}
else
{
}
if (jvseq instanceof SequenceI)
{
- leaf.setElement((SequenceI)jvseq);
+ leaf.setElement((SequenceI) jvseq);
leaf.setPlaceholder(false);
}
else
{
if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
{
- Object assocseq = ((BinaryNode) tnode)
- .element();
+ Object assocseq = ((BinaryNode) tnode).element();
if (assocseq instanceof SequenceI)
{
Vobject vobj = this.getjv2vObj(assocseq);
protected StringBuilder errorWarning = new StringBuilder();
- protected JButton btn_cancel;
+ protected JButton btn_cancel;
+
protected JButton btn_add;
protected JButton btn_newView;
}
});
- btn_cancel = new JButton(
- MessageManager.getString("action.cancel"));
+ btn_cancel = new JButton(MessageManager.getString("action.cancel"));
btn_cancel.setFont(VERDANA_12);
btn_cancel.addActionListener(new ActionListener()
{
lbl_pdbFile.setFont(VERDANA_10);
lbl_chooseTempFacType.setFont(VERDANA_12);
- lbl_chooseTempFacType.setText(MessageManager.getString("label.interpret_tempfac_as"));
+ lbl_chooseTempFacType.setText(
+ MessageManager.getString("label.interpret_tempfac_as"));
combo_tempFacAs.setFont(VERDANA_12);
for (TFType t : TFType.values())
});
btn_paeMatrixFile.setFont(VERDANA_12);
- btn_paeMatrixFile.setText(MessageManager.getString("label.add_pae_matrix_file"));
+ btn_paeMatrixFile
+ .setText(MessageManager.getString("label.add_pae_matrix_file"));
btn_paeMatrixFile.addActionListener(new ActionListener()
{
@Override
gbc.gridy++;
gbc.insets = new Insets(0, 0, 2, 0);
- pnl_fileOptions.add(new JLabel(MessageManager.getString("label.structure_import_options")), gbc);
+ pnl_fileOptions.add(new JLabel(
+ MessageManager.getString("label.structure_import_options")),
+ gbc);
gbc.gridy++;
-
+
gbc.insets = new Insets(0, 0, 6, 0);
pnl_fileOptions.add(lbl_chooseTempFacType, gbc);
gbc.gridy++;
ov.getCanvas().getResidueColour().getRGB());
overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
view.setOverview(overview);
- }
+ }
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
line.setColour(annotation.getThreshold().colour.getRGB());
an.setThresholdLine(line);
}
- if (annotation.graph==AlignmentAnnotation.CONTACT_MAP)
+ if (annotation.graph == AlignmentAnnotation.CONTACT_MAP)
{
- if (annotation.sequenceRef.getContactMaps()!=null)
+ if (annotation.sequenceRef.getContactMaps() != null)
{
- ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation);
- if (cm!=null)
+ ContactMatrixI cm = annotation.sequenceRef
+ .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 ?
+ // 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())
+ for (BitSet gp : cm.getGroups())
{
xmlmat.getGroups().add(stringifyBitset(gp));
}
{
xmlmat.setCutHeight(cm.getCutHeight());
}
-
+
// set/get properties
if (cm instanceof MappableContactMatrixI)
{
}
- private String stringifyBitset(BitSet gp) {
+ private String stringifyBitset(BitSet gp)
+ {
StringBuilder sb = new StringBuilder();
- for (long val:gp.toLongArray())
+ for (long val : gp.toLongArray())
{
- if (sb.length()>0) {
+ if (sb.length() > 0)
+ {
sb.append(",");
}
sb.append(val);
}
return sb.toString();
}
- private BitSet deStringifyBitset(String stringified) {
- if ("".equals(stringified) || stringified==null)
+
+ private BitSet deStringifyBitset(String stringified)
+ {
+ if ("".equals(stringified) || stringified == null)
{
return new BitSet();
}
String[] longvals = stringified.split(",");
long[] newlongvals = new long[longvals.length];
- for (int lv=0;lv<longvals.length;lv++)
+ for (int lv = 0; lv < longvals.length; lv++)
{
- try {
- newlongvals[lv]=Long.valueOf(longvals[lv]);
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
} catch (Exception x)
{
- errorMessage+="Couldn't destringify bitset from: '"+stringified+"'";
- newlongvals[lv]=0;
+ errorMessage += "Couldn't destringify bitset from: '" + stringified
+ + "'";
+ newlongvals[lv] = 0;
}
}
return BitSet.valueOf(newlongvals);
-
}
+
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
}
return vamsasSeq;
}
-
+
private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
SequenceI parentseq, SequenceI jds, boolean recurse)
{
jaa.setCalcId(annotation.getCalcId());
if (annotation.getProperty().size() > 0)
{
- for (jalview.xml.binding.jalview.Property prop : annotation.getProperty())
+ for (jalview.xml.binding.jalview.Property prop : annotation
+ .getProperty())
{
jaa.setProperty(prop.getName(), prop.getValue());
}
xmlmat.getCols().intValue(),
xmlmat.getRows().intValue());
jalview.util.MapList mapping = null;
- if (xmlmat.getMapping()!=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();
+ Iterator<MapListFrom> from = m.getMapListFrom()
+ .iterator();// enumerateMapListFrom();
for (int _i = 0; from.hasNext(); _i += 2)
{
MapListFrom mf = from.next();
fto[_i + 1] = mf.getEnd();
}
- mapping = new jalview.util.MapList(fr, fto, m.getMapFromUnit().intValue(),m.getMapToUnit().intValue());
+ mapping = new jalview.util.MapList(fr, fto,
+ m.getMapFromUnit().intValue(),
+ m.getMapToUnit().intValue());
}
- List<BitSet> newgroups=new ArrayList<BitSet>();
- if (xmlmat.getGroups().size()>0)
+ List<BitSet> newgroups = new ArrayList<BitSet>();
+ if (xmlmat.getGroups().size() > 0)
{
- for (String sgroup:xmlmat.getGroups())
+ 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)
+ 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;
+ 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, mapping, elements, grpset);
jaa.sequenceRef.addContactListFor(jaa, newpae);
}
}
*/
protected void loadOverview(Viewport view, String version, AlignFrame af)
{
- if (!isVersionStringLaterThan("2.11.3",
- version) && view.getOverview()==null)
+ if (!isVersionStringLaterThan("2.11.3", version)
+ && view.getOverview() == null)
{
return;
}
{
if (tree.isColumnWise())
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds.get(tree
- .getColumnReference());
+ AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds
+ .get(tree.getColumnReference());
if (aa == null)
{
Console.warn(
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
- viewport.setFont(new Font(view.getFontName(),
- safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
- (view.getCharWidth()!=null) ? false : true);
- if (view.getCharWidth()!=null)
+ viewport.setFont(
+ new Font(view.getFontName(), safeInt(view.getFontStyle()),
+ safeInt(view.getFontSize())),
+ (view.getCharWidth() != null) ? false : true);
+ if (view.getCharWidth() != null)
{
viewport.setCharWidth(view.getCharWidth());
viewport.setCharHeight(view.getCharHeight());
+ annotationId);
return null;
}
- // belt-and-braces create a threshold line if the
+ // belt-and-braces create a threshold line if the
// colourscheme needs one but the matchedAnnotation doesn't have one
if (safeInt(viewAnnColour.getAboveThreshold()) != 0
&& matchedAnnotation.getThreshold() == null)
.getRendererFor(row);
if (renderer != null)
{
- renderer.renderRow(g, charWidth, charHeight,
- hasHiddenColumns, av, hiddenColumns, columnSelection,
- row, row_annotations, startRes, endRes, row.graphMin,
+ renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns,
+ av, hiddenColumns, columnSelection, row,
+ row_annotations, startRes, endRes, row.graphMin,
row.graphMax, y);
}
if (debugRedraw)
{
if (renderer == null)
{
- System.err.println("No renderer found for "
- + row.toString());
+ System.err
+ .println("No renderer found for " + row.toString());
}
else
{
- System.err.println("rendered with "
- + renderer.getClass().toString());
+ System.err.println(
+ "rendered with " + renderer.getClass().toString());
}
}
import java.util.IdentityHashMap;
-public class AnnotationRendererFactory implements
- AnnotationRendererFactoryI
+public class AnnotationRendererFactory implements AnnotationRendererFactoryI
{
private static AnnotationRendererFactoryI factory = null;
{
return ContactMapRenderer.newPAERenderer();
}
- // TODO add potential for configuring renderer directly from the annotation row and/or viewmodel
-
+ // TODO add potential for configuring renderer directly from the
+ // annotation row and/or viewmodel
+
}
return null;
}
*/
public class ContactGeometry
{
-
+
final ContactListI contacts;
-
+
final int pixels_step;
final double contacts_per_pixel;
public ContactGeometry(final ContactListI contacts, int graphHeight)
{
- this.contacts=contacts;
+ this.contacts = contacts;
this.graphHeight = graphHeight;
contact_height = contacts.getContactHeight();
// fractional number of contacts covering each pixel
public final int pEnd;
}
+
/**
*
* @param columnSelection
* @param ci
- * @param visibleOnly - when true, only test intersection of visible columns given matrix range
- * @return true if the range on the matrix specified by ci intersects with selected columns in the ContactListI's reference frame.
+ * @param visibleOnly
+ * - when true, only test intersection of visible columns given
+ * matrix range
+ * @return true if the range on the matrix specified by ci intersects with
+ * selected columns in the ContactListI's reference frame.
*/
-
+
boolean intersects(contactInterval ci, ColumnSelection columnSelection,
HiddenColumns hiddenColumns, boolean visibleOnly)
{
{
/**
* bean holding colours for shading
+ *
* @author jprocter
*
*/
* shown when no data available from map
*/
Color no_data;
+
/**
* shown for region not currently visible - should normally not see this
*/
Color hidden;
+
/**
* linear shading scheme min/max
*/
/**
* build an EBI-AlphaFold style renderer of PAE matrices
+ *
* @return
*/
public static ContactMapRenderer newPAERenderer()
continue;
}
// ContactListI from viewport can map column -> group
- Color gpcol = (cm==null) ? Color.white: contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
-
+ Color gpcol = (cm == null) ? Color.white
+ : contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
+
// feature still in development - highlight or omit regions hidden in
// the alignment - currently marks them as red rows
boolean maskHiddenCols = false;
- // TODO: optionally pass visible column mask to the ContactGeometry object so it maps
+ // TODO: optionally pass visible column mask to the ContactGeometry object
+ // so it maps
// only visible contacts to geometry
// Bean holding mapping from contact list to pixels
- // TODO: allow bracketing/limiting of range on contacts to render (like visible column mask but more flexible?)
-
+ // TODO: allow bracketing/limiting of range on contacts to render (like
+ // visible column mask but more flexible?)
+
// COntactListI provides mapping for column -> cm-groupmapping
final ContactGeometry cgeom = new ContactGeometry(contacts,
_aa.graphHeight);
for (int ht = y2, eht = y2
- _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
{
-
+
ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
y2 - ht + cgeom.pixels_step);
// cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
boolean rowsel = false, containsHidden = false;
if (columnSelection != null)
{
- rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, maskHiddenCols);
+ rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+ maskHiddenCols);
}
// TODO: show selected region
if (colsel || rowsel)
{
col = shade.hidden;
}
- if (gpcol!=null && gpcol!=Color.white) {
+ if (gpcol != null && gpcol != Color.white)
+ {
// todo - could overlay group as a transparent rectangle ?
- col = new Color((int)(((float)(col.getRed()+gpcol.getRed()))/2f),
- (int)(((float)(col.getGreen()+gpcol.getGreen()))/2f),
- (int)(((float)(col.getBlue()+gpcol.getBlue()))/2f));
+ col = new Color(
+ (int) (((float) (col.getRed() + gpcol.getRed())) / 2f),
+ (int) (((float) (col.getGreen() + gpcol.getGreen()))
+ / 2f),
+ (int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
}
g.setColor(col);
-
+
if (cgeom.pixels_step > 1)
{
g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
Color shadeFor(float min, float max, float value)
{
- return jalview.util.ColorUtils.getGraduatedColour(value, 0, shade.minColor,
- max, shade.maxColor);
+ return jalview.util.ColorUtils.getGraduatedColour(value, 0,
+ shade.minColor, max, shade.maxColor);
}
public Color getColorForRange(float min, float max, ContactListI cl,
/**
* Constructor without colour settings (used by applet)
+ *
* @deprecated
*/
@Deprecated
void renderRow(Graphics g, int charWidth, int charHeight,
boolean hasHiddenColumns, AlignViewportI av,
- HiddenColumns hiddenColumns,
- ColumnSelection columnSelection, AlignmentAnnotation row,
- Annotation[] row_annotations, int startRes, int endRes,
- float graphMin, float graphMax, int y);
+ HiddenColumns hiddenColumns, ColumnSelection columnSelection,
+ AlignmentAnnotation row, Annotation[] row_annotations,
+ int startRes, int endRes, float graphMin, float graphMax, int y);
}
*/
List<SequenceFeature> overlaps = seq.findFeatures(column, column,
type);
- for (int i = overlaps.size() - 1 ; i >= 0 ; i--)
+ for (int i = overlaps.size() - 1; i >= 0; i--)
{
SequenceFeature sequenceFeature = overlaps.get(i);
if (!featureGroupNotShown(sequenceFeature))
}
List<StructureCommandI> finalView = commandGenerator
.centerViewOn(models);
- if (finalView!=null && finalView.size()>0)
+ if (finalView != null && finalView.size() > 0)
{
executeCommands(finalView, false, "Centered on Superposition");
}
return alignment.getContactMatrixFor(alignmentAnnotation);
}
-
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
boolean hasReferenceSeq();
SequenceI getReferenceSeq();
+
/**
* remaps the matrix to a new reference sequence
- * @param dsq
- * @param sqmpping - mapping from current reference to new reference - 1:1 only
+ *
+ * @param dsq
+ * @param sqmpping
+ * - mapping from current reference to new reference - 1:1 only
* @return new ContactMatrixI instance with updated mapping
*/
MappableContactMatrixI liftOver(SequenceI dsq, Mapping sqmpping);
-
+
/**
* like ContactMatrixI.getContactList(int column) but
- * @param localFrame - sequence or other object that this contact matrix is associated with
- * @param column - position in localFrame
+ *
+ * @param localFrame
+ * - sequence or other object that this contact matrix is associated
+ * with
+ * @param column
+ * - position in localFrame
* @return ContactListI that returns contacts w.r.t. localFrame
*/
-
+
ContactListI getMappableContactList(SequenceI localFrame, int column);
/**
*
- * Similar to AlignedCodonFrame.getMappingBetween
+ * Similar to AlignedCodonFrame.getMappingBetween
*
- * @param sequenceRef - a reference sequence mappable to this contactMatrix - may be null
- * @return null or the MapList mapping to the coordinates of the reference sequence (or if hasReferenceSeq() is false, and sequenceRef is null, any mapping present)
+ * @param sequenceRef
+ * - a reference sequence mappable to this contactMatrix - may be
+ * null
+ * @return null or the MapList mapping to the coordinates of the reference
+ * sequence (or if hasReferenceSeq() is false, and sequenceRef is
+ * null, any mapping present)
*
*/
MapList getMapFor(SequenceI sequenceRef);
-
+
/**
* Locate a position in the mapped sequence for a column in the matrix - use
* this to resolve positions corresponding to column clusters
import jalview.util.MapList;
import jalview.ws.datamodel.MappableContactMatrixI;
-public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>> implements MappableContactMatrixI
+public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
+ implements MappableContactMatrixI
{
SequenceI refSeq = null;
+
MapList toSeq = null;
/**
*/
int length;
-
@Override
public boolean hasReferenceSeq()
{
{
return refSeq;
}
+
/**
* container for groups - defined on matrix columns
*/
- GroupSet grps=new GroupSet();
+ GroupSet grps = new GroupSet();
+
@Override
public GroupSetI getGroupSet()
{
return grps;
};
+
@Override
public void setGroupSet(GroupSet makeGroups)
{
@Override
public MapList getMapFor(SequenceI mapSeq)
{
- if (refSeq!=null)
+ if (refSeq != null)
{
- while (mapSeq!=refSeq && mapSeq.getDatasetSequence()!=null)
+ while (mapSeq != refSeq && mapSeq.getDatasetSequence() != null)
{
mapSeq = mapSeq.getDatasetSequence();
}
- if (mapSeq!=refSeq)
+ if (mapSeq != refSeq)
{
return null;
}
- } else {
- if (mapSeq!=null) {
+ }
+ else
+ {
+ if (mapSeq != null)
+ {
// our MapList does not concern this seq
return null;
}
}
-
+
return toSeq;
}
/**
- * set the reference sequence and construct the mapping between the start-end positions of given sequence and row/columns of contact matrix
+ * set the reference sequence and construct the mapping between the start-end
+ * positions of given sequence and row/columns of contact matrix
+ *
* @param _refSeq
*/
public void setRefSeq(SequenceI _refSeq)
refSeq = refSeq.getDatasetSequence();
}
length = _refSeq.getEnd() - _refSeq.getStart() + 1;
-// if (length!=refSeq.getLength() || _refSeq.getStart()!=1)
+ // if (length!=refSeq.getLength() || _refSeq.getStart()!=1)
{
- toSeq = new MapList(new int[] { _refSeq.getStart(), _refSeq.getEnd()}, new int[] { 0,length-1}, 1,1);
+ toSeq = new MapList(
+ new int[]
+ { _refSeq.getStart(), _refSeq.getEnd() },
+ new int[]
+ { 0, length - 1 }, 1, 1);
}
}
return newCM;
}
- protected abstract T newMappableContactMatrix(SequenceI newRefSeq,
+ protected abstract T newMappableContactMatrix(SequenceI newRefSeq,
MapList newFromMapList);
+
@Override
public int[] getMappedPositionsFor(final SequenceI localFrame,
final int column)
{
- return getMappedPositionsFor(localFrame,column,column);
+ return getMappedPositionsFor(localFrame, column, column);
}
- public int[] getMappedPositionsFor(final SequenceI localFrame,
- int from,int to)
+
+ public int[] getMappedPositionsFor(final SequenceI localFrame, int from,
+ int to)
{
- if (localFrame==null)
+ if (localFrame == null)
{
throw new Error("Unimplemented when no local sequence given.");
}
// return a ContactListI for column
// column is index into localFrame
// 1. map column to corresponding column in matrix
-
- final int _lcolumn=localFrame.findPosition(from);
- final int _rcolumn=(from==to) ? _lcolumn:localFrame.findPosition(to);
+
+ final int _lcolumn = localFrame.findPosition(from);
+ final int _rcolumn = (from == to) ? _lcolumn
+ : localFrame.findPosition(to);
if (toSeq == null)
{
// no mapping
- return new int[] { _lcolumn,_rcolumn};
+ return new int[] { _lcolumn, _rcolumn };
}
SequenceI lf = localFrame, uf = refSeq;
+ "' is not mappable for the given localFrame sequence. ("
+ localFrame.getName() + ")");
}
-
- int[] mappedPositions = toSeq.locateInFrom(_lcolumn,_rcolumn);
+
+ int[] mappedPositions = toSeq.locateInFrom(_lcolumn, _rcolumn);
// TODO - trim to localFrame ?
-// if (mappedPositions!=null) {
-// int s=-1,e=-1;
-// for (int p=0;p<mappedPositions.length;p++)
-// {
-// if (s==-1 && mappedPositions[p]>=localFrame.getStart())
-// {
-// s=p; // remember first position within local frame
-// }
-// if (e==-1 || mappedPositions[p]<=localFrame.getEnd())
-// {
-// // update end pointer
-// e=p;
-// // compute local map
-// mappedPositions[p] = localFrame.findIndex(mappedPositions[p]);
-// }
-// }
-// }
+ // if (mappedPositions!=null) {
+ // int s=-1,e=-1;
+ // for (int p=0;p<mappedPositions.length;p++)
+ // {
+ // if (s==-1 && mappedPositions[p]>=localFrame.getStart())
+ // {
+ // s=p; // remember first position within local frame
+ // }
+ // if (e==-1 || mappedPositions[p]<=localFrame.getEnd())
+ // {
+ // // update end pointer
+ // e=p;
+ // // compute local map
+ // mappedPositions[p] = localFrame.findIndex(mappedPositions[p]);
+ // }
+ // }
+ // }
return mappedPositions;
}
{
final int _column;
final int _lcolumn;
- if (localFrame==null)
+ if (localFrame == null)
{
throw new Error("Unimplemented when no local sequence given.");
}
// return a ContactListI for column
// column is index into localFrame
// 1. map column to corresponding column in matrix
- final MappableContactMatrix us=this;
- _lcolumn=localFrame.findPosition(column);
-
+ final MappableContactMatrix us = this;
+ _lcolumn = localFrame.findPosition(column);
+
if (toSeq != null)
{
SequenceI lf = localFrame, uf = refSeq;
}
else
{
- // no mapping
+ // no mapping
_column = _lcolumn;
}
- // TODO - remove ? this may be a redundant check
+ // TODO - remove ? this may be a redundant check
if (_column < 0 || ((toSeq != null && _column > toSeq.getToHighest())
|| (toSeq == null && getHeight() <= _column)))
{
int h = 0;
for (int p = 0; p < matrixRange.length; p += 2)
{
- h += 1+Math.abs(matrixRange[p + 1] - matrixRange[p]);
+ h += 1 + Math.abs(matrixRange[p + 1] - matrixRange[p]);
}
final int rangeHeight = h;
// 3. Construct ContactListImpl instance for just those segments.
-
+
return new ContactListImpl(new ContactListProviderI()
{
}
return matrixRange[p] + mcolumn - h;
}
+
@Override
public Color getColourForGroup()
{
/**
* get a specific element of the 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
+ * rather than the mapped frame. Implementations are allowed to throw
+ * RunTimeExceptions if _column/i are out of bounds
*
* @param _column
* @param i
* @return
*/
protected abstract double getElementAt(int _column, int i);
-
+
}
import jalview.util.MapUtils;
import jalview.ws.dbsources.EBIAlfaFold;
-public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
+public class PAEContactMatrix extends
+ MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
{
int maxrow = 0, maxcol = 0;
float maxscore;
-
@SuppressWarnings("unchecked")
- public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws FileFormatException
+ public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+ throws FileFormatException
{
setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
/**
* new matrix with specific mapping to a reference sequence
+ *
* @param newRefSeq
* @param newFromMapList
* @param elements2
- * @param grps2
+ * @param grps2
*/
- public PAEContactMatrix(SequenceI newRefSeq,
- MapList newFromMapList, float[][] elements2, GroupSet grps2)
+ public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
+ float[][] elements2, GroupSet grps2)
{
- this(newRefSeq,elements2);
+ this(newRefSeq, elements2);
toSeq = newFromMapList;
- grps= grps2;
+ grps = grps2;
}
/**
{
elements[row][col++] = (float) ((Long) d).longValue();
}
-
+
if (maxscore < elements[row][col - 1])
{
maxscore = elements[row][col - 1];
@Override
public ContactListI getContactList(final int column)
{
-// final int _column;
-// if (toSeq != null)
-// {
-// int[] word = toSeq.locateInTo(column, column);
-// if (word == null)
-// {
-// return null;
-// }
-// _column = word[0];
-// }
-// else
-// {
-// _column = column;
-// }
+ // final int _column;
+ // if (toSeq != null)
+ // {
+ // int[] word = toSeq.locateInTo(column, column);
+ // if (word == null)
+ // {
+ // return null;
+ // }
+ // _column = word[0];
+ // }
+ // else
+ // {
+ // _column = column;
+ // }
if (column < 0 || column >= elements.length)
{
return null;
{
return elements[_column][i];
}
+
@Override
public float getMin()
{
@Override
public String getAnnotDescr()
{
- return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
+ return "Predicted Alignment Error"
+ + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
}
@Override
public String getAnnotLabel()
{
StringBuilder label = new StringBuilder("PAE Matrix");
- //if (this.getReferenceSeq() != null)
- //{
- // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
- //}
+ // if (this.getReferenceSeq() != null)
+ // {
+ // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ // }
return label.toString();
}
{
return length;
}
-
- public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException
+
+ public static void validateContactMatrixFile(String fileName)
+ throws FileFormatException, IOException
{
- FileInputStream infile=null;
- try {
+ FileInputStream infile = null;
+ try
+ {
infile = new FileInputStream(new File(fileName));
} catch (Throwable t)
{
- new IOException("Couldn't open "+fileName,t);
+ new IOException("Couldn't open " + fileName, t);
}
-
-
- JSONObject paeDict=null;
- try {
+
+ JSONObject paeDict = null;
+ try
+ {
paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile);
} catch (Throwable t)
{
- new FileFormatException("Couldn't parse "+fileName+" as a JSON dict or array containing a dict");
+ new FileFormatException("Couldn't parse " + fileName
+ + " as a JSON dict or array containing a dict");
}
-
- PAEContactMatrix matrix = new PAEContactMatrix(new SequenceDummy("Predicted"), (Map<String,Object>)paeDict);
- if (matrix.getWidth()<=0)
+
+ PAEContactMatrix matrix = new PAEContactMatrix(
+ new SequenceDummy("Predicted"), (Map<String, Object>) paeDict);
+ if (matrix.getWidth() <= 0)
{
- throw new FileFormatException("No data in PAE matrix read from '"+fileName+"'");
+ throw new FileFormatException(
+ "No data in PAE matrix read from '" + fileName + "'");
}
}
@Override
- protected PAEContactMatrix newMappableContactMatrix(
- SequenceI newRefSeq, MapList newFromMapList)
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
{
- PAEContactMatrix pae=new PAEContactMatrix(newRefSeq, newFromMapList,
- elements, new GroupSet(grps));
+ PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
+ elements, new GroupSet(grps));
return pae;
- }
+ }
}
ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
(Map<String, Object>) pae_obj);
- matrix.setGroupSet(GroupSet.makeGroups(matrix,5f, true));
+ matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
sm.getSequence().addAlignmentAnnotation(cmannot);
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.embl;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for EntrySetType complex type.
+ * <p>
+ * Java class for EntrySetType 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="EntrySetType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntrySetType", propOrder = {
- "entry"
-})
-public class EntrySetType {
+@XmlType(name = "EntrySetType", propOrder = { "entry" })
+public class EntrySetType
+{
- @XmlElement(required = true)
- protected List<EntryType> entry;
+ @XmlElement(required = true)
+ protected List<EntryType> entry;
- /**
- * Gets the value of the entry 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 entry property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEntry().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType }
- *
- *
- */
- public List<EntryType> getEntry() {
- if (entry == null) {
- entry = new ArrayList<EntryType>();
- }
- return this.entry;
+ /**
+ * Gets the value of the entry 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 entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link EntryType }
+ *
+ *
+ */
+ public List<EntryType> getEntry()
+ {
+ if (entry == null)
+ {
+ entry = new ArrayList<EntryType>();
}
+ return this.entry;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.embl;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlType;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <p>Java class for EntryType complex type.
+ * <p>
+ * Java class for EntryType 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="EntryType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntryType", propOrder = {
- "secondaryAccession",
- "projectAccession",
- "description",
- "comment",
- "keyword",
- "reference",
- "xref",
- "feature",
- "assembly",
- "contig",
- "sequence"
-})
-public class EntryType {
-
- protected List<String> secondaryAccession;
- protected List<String> projectAccession;
+@XmlType(
+ name = "EntryType",
+ propOrder =
+ { "secondaryAccession", "projectAccession", "description", "comment",
+ "keyword", "reference", "xref", "feature", "assembly", "contig",
+ "sequence" })
+public class EntryType
+{
+
+ protected List<String> secondaryAccession;
+
+ protected List<String> projectAccession;
+
+ @XmlElement(required = true)
+ protected String description;
+
+ protected String comment;
+
+ protected List<String> keyword;
+
+ protected List<EntryType.Reference> reference;
+
+ protected List<XrefType> xref;
+
+ protected List<EntryType.Feature> feature;
+
+ protected EntryType.Assembly assembly;
+
+ protected EntryType.Contig contig;
+
+ protected String sequence;
+
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+
+ @XmlAttribute(name = "entryVersion")
+ protected BigInteger entryVersion;
+
+ @XmlAttribute(name = "dataClass", required = true)
+ protected String dataClass;
+
+ @XmlAttribute(name = "taxonomicDivision", required = true)
+ protected String taxonomicDivision;
+
+ @XmlAttribute(name = "moleculeType", required = true)
+ protected String moleculeType;
+
+ @XmlAttribute(name = "sequenceLength", required = true)
+ protected BigInteger sequenceLength;
+
+ @XmlAttribute(name = "topology", required = true)
+ protected String topology;
+
+ @XmlAttribute(name = "firstPublic")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar firstPublic;
+
+ @XmlAttribute(name = "firstPublicRelease")
+ protected BigInteger firstPublicRelease;
+
+ @XmlAttribute(name = "lastUpdated")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar lastUpdated;
+
+ @XmlAttribute(name = "lastUpdatedRelease")
+ protected BigInteger lastUpdatedRelease;
+
+ /**
+ * Gets the value of the secondaryAccession 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 secondaryAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSecondaryAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getSecondaryAccession()
+ {
+ if (secondaryAccession == null)
+ {
+ secondaryAccession = new ArrayList<String>();
+ }
+ return this.secondaryAccession;
+ }
+
+ /**
+ * Gets the value of the projectAccession 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 projectAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getProjectAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getProjectAccession()
+ {
+ if (projectAccession == null)
+ {
+ projectAccession = new ArrayList<String>();
+ }
+ return this.projectAccession;
+ }
+
+ /**
+ * 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 comment property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComment()
+ {
+ return comment;
+ }
+
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComment(String value)
+ {
+ this.comment = value;
+ }
+
+ /**
+ * Gets the value of the keyword 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 keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getKeyword()
+ {
+ if (keyword == null)
+ {
+ keyword = new ArrayList<String>();
+ }
+ return this.keyword;
+ }
+
+ /**
+ * Gets the value of the reference 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 reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Reference }
+ *
+ *
+ */
+ public List<EntryType.Reference> getReference()
+ {
+ if (reference == null)
+ {
+ reference = new ArrayList<EntryType.Reference>();
+ }
+ return this.reference;
+ }
+
+ /**
+ * Gets the value of the xref 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 xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref()
+ {
+ if (xref == null)
+ {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the feature 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 feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature }
+ *
+ *
+ */
+ public List<EntryType.Feature> getFeature()
+ {
+ if (feature == null)
+ {
+ feature = new ArrayList<EntryType.Feature>();
+ }
+ return this.feature;
+ }
+
+ /**
+ * Gets the value of the assembly property.
+ *
+ * @return possible object is {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly getAssembly()
+ {
+ return assembly;
+ }
+
+ /**
+ * Sets the value of the assembly property.
+ *
+ * @param value
+ * allowed object is {@link EntryType.Assembly }
+ *
+ */
+ public void setAssembly(EntryType.Assembly value)
+ {
+ this.assembly = value;
+ }
+
+ /**
+ * Gets the value of the contig property.
+ *
+ * @return possible object is {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig getContig()
+ {
+ return contig;
+ }
+
+ /**
+ * Sets the value of the contig property.
+ *
+ * @param value
+ * allowed object is {@link EntryType.Contig }
+ *
+ */
+ public void setContig(EntryType.Contig value)
+ {
+ this.contig = value;
+ }
+
+ /**
+ * 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 accession property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAccession(String value)
+ {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the entryVersion property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEntryVersion()
+ {
+ return entryVersion;
+ }
+
+ /**
+ * Sets the value of the entryVersion property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEntryVersion(BigInteger value)
+ {
+ this.entryVersion = value;
+ }
+
+ /**
+ * Gets the value of the dataClass property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDataClass()
+ {
+ return dataClass;
+ }
+
+ /**
+ * Sets the value of the dataClass property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDataClass(String value)
+ {
+ this.dataClass = value;
+ }
+
+ /**
+ * Gets the value of the taxonomicDivision property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTaxonomicDivision()
+ {
+ return taxonomicDivision;
+ }
+
+ /**
+ * Sets the value of the taxonomicDivision property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTaxonomicDivision(String value)
+ {
+ this.taxonomicDivision = value;
+ }
+
+ /**
+ * Gets the value of the moleculeType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMoleculeType()
+ {
+ return moleculeType;
+ }
+
+ /**
+ * Sets the value of the moleculeType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMoleculeType(String value)
+ {
+ this.moleculeType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceLength property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getSequenceLength()
+ {
+ return sequenceLength;
+ }
+
+ /**
+ * Sets the value of the sequenceLength property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setSequenceLength(BigInteger value)
+ {
+ this.sequenceLength = value;
+ }
+
+ /**
+ * Gets the value of the topology property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTopology()
+ {
+ return topology;
+ }
+
+ /**
+ * Sets the value of the topology property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTopology(String value)
+ {
+ this.topology = value;
+ }
+
+ /**
+ * Gets the value of the firstPublic property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getFirstPublic()
+ {
+ return firstPublic;
+ }
+
+ /**
+ * Sets the value of the firstPublic property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setFirstPublic(XMLGregorianCalendar value)
+ {
+ this.firstPublic = value;
+ }
+
+ /**
+ * Gets the value of the firstPublicRelease property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getFirstPublicRelease()
+ {
+ return firstPublicRelease;
+ }
+
+ /**
+ * Sets the value of the firstPublicRelease property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setFirstPublicRelease(BigInteger value)
+ {
+ this.firstPublicRelease = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdated property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getLastUpdated()
+ {
+ return lastUpdated;
+ }
+
+ /**
+ * Sets the value of the lastUpdated property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setLastUpdated(XMLGregorianCalendar value)
+ {
+ this.lastUpdated = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdatedRelease property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getLastUpdatedRelease()
+ {
+ return lastUpdatedRelease;
+ }
+
+ /**
+ * Sets the value of the lastUpdatedRelease property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setLastUpdatedRelease(BigInteger value)
+ {
+ this.lastUpdatedRelease = 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="range" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "range" })
+ public static class Assembly
+ {
+
@XmlElement(required = true)
- protected String description;
- protected String comment;
- protected List<String> keyword;
- protected List<EntryType.Reference> reference;
- protected List<XrefType> xref;
- protected List<EntryType.Feature> feature;
- protected EntryType.Assembly assembly;
- protected EntryType.Contig contig;
- protected String sequence;
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
- @XmlAttribute(name = "entryVersion")
- protected BigInteger entryVersion;
- @XmlAttribute(name = "dataClass", required = true)
- protected String dataClass;
- @XmlAttribute(name = "taxonomicDivision", required = true)
- protected String taxonomicDivision;
- @XmlAttribute(name = "moleculeType", required = true)
- protected String moleculeType;
- @XmlAttribute(name = "sequenceLength", required = true)
- protected BigInteger sequenceLength;
- @XmlAttribute(name = "topology", required = true)
- protected String topology;
- @XmlAttribute(name = "firstPublic")
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar firstPublic;
- @XmlAttribute(name = "firstPublicRelease")
- protected BigInteger firstPublicRelease;
- @XmlAttribute(name = "lastUpdated")
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar lastUpdated;
- @XmlAttribute(name = "lastUpdatedRelease")
- protected BigInteger lastUpdatedRelease;
+ protected List<EntryType.Assembly.Range> range;
/**
- * Gets the value of the secondaryAccession property.
+ * Gets the value of the range 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 secondaryAccession property.
+ * 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 range property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getSecondaryAccession().add(newItem);
+ * getRange().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link String }
+ * {@link EntryType.Assembly.Range }
*
*
*/
- public List<String> getSecondaryAccession() {
- if (secondaryAccession == null) {
- secondaryAccession = new ArrayList<String>();
- }
- return this.secondaryAccession;
+ public List<EntryType.Assembly.Range> getRange()
+ {
+ if (range == null)
+ {
+ range = new ArrayList<EntryType.Assembly.Range>();
+ }
+ return this.range;
}
/**
- * Gets the value of the projectAccession 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 projectAccession property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getProjectAccession().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
*/
- public List<String> getProjectAccession() {
- if (projectAccession == null) {
- projectAccession = new ArrayList<String>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range
+ {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin()
+ {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value)
+ {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd()
+ {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value)
+ {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAccession(String value)
+ {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isComplement()
+ {
+ if (complement == null)
+ {
+ return false;
}
- return this.projectAccession;
- }
-
- /**
- * 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;
- }
+ else
+ {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value)
+ {
+ this.complement = value;
+ }
- /**
- * Gets the value of the comment property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComment() {
- return comment;
}
- /**
- * Sets the value of the comment property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setComment(String value) {
- this.comment = 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>
+ * <choice maxOccurs="unbounded" minOccurs="0">
+ * <element name="range">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="gap">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "rangeOrGap" })
+ public static class Contig
+ {
+
+ @XmlElements({
+ @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+ @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) })
+ protected List<Object> rangeOrGap;
/**
- * Gets the value of the keyword property.
+ * Gets the value of the rangeOrGap 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 keyword property.
+ * 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 rangeOrGap property.
*
* <p>
* For example, to add a new item, do as follows:
- * <pre>
- * getKeyword().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getKeyword() {
- if (keyword == null) {
- keyword = new ArrayList<String>();
- }
- return this.keyword;
- }
-
- /**
- * Gets the value of the reference 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 reference property.
*
- * <p>
- * For example, to add a new item, do as follows:
* <pre>
- * getReference().add(newItem);
+ * getRangeOrGap().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EntryType.Reference }
+ * {@link EntryType.Contig.Range } {@link EntryType.Contig.Gap }
*
*
*/
- public List<EntryType.Reference> getReference() {
- if (reference == null) {
- reference = new ArrayList<EntryType.Reference>();
- }
- return this.reference;
+ public List<Object> getRangeOrGap()
+ {
+ if (rangeOrGap == null)
+ {
+ rangeOrGap = new ArrayList<Object>();
+ }
+ return this.rangeOrGap;
}
/**
- * Gets the value of the xref 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 xref property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getXref().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link XrefType }
- *
- *
*/
- public List<XrefType> getXref() {
- if (xref == null) {
- xref = new ArrayList<XrefType>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Gap
+ {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+
+ @XmlAttribute(name = "length", required = true)
+ protected BigInteger length;
+
+ @XmlAttribute(name = "unknownLength")
+ protected Boolean unknownLength;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getLength()
+ {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setLength(BigInteger value)
+ {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the unknownLength property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isUnknownLength()
+ {
+ if (unknownLength == null)
+ {
+ return false;
+ }
+ else
+ {
+ return unknownLength;
}
- return this.xref;
+ }
+
+ /**
+ * Sets the value of the unknownLength property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setUnknownLength(Boolean value)
+ {
+ this.unknownLength = value;
+ }
+
}
/**
- * Gets the value of the feature 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 feature property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getFeature().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature }
- *
- *
*/
- public List<EntryType.Feature> getFeature() {
- if (feature == null) {
- feature = new ArrayList<EntryType.Feature>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range
+ {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin()
+ {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value)
+ {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd()
+ {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value)
+ {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAccession(String value)
+ {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isComplement()
+ {
+ if (complement == null)
+ {
+ return false;
}
- return this.feature;
- }
+ else
+ {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value)
+ {
+ this.complement = value;
+ }
- /**
- * Gets the value of the assembly property.
- *
- * @return
- * possible object is
- * {@link EntryType.Assembly }
- *
- */
- public EntryType.Assembly getAssembly() {
- return assembly;
}
- /**
- * Sets the value of the assembly property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Assembly }
- *
- */
- public void setAssembly(EntryType.Assembly value) {
- this.assembly = 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="taxon" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "taxon", "xref", "qualifier" })
+ public static class Feature
+ {
+
+ protected EntryType.Feature.FeatureTaxon taxon;
- /**
- * Gets the value of the contig property.
- *
- * @return
- * possible object is
- * {@link EntryType.Contig }
- *
- */
- public EntryType.Contig getContig() {
- return contig;
- }
+ protected List<XrefType> xref;
- /**
- * Sets the value of the contig property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Contig }
- *
- */
- public void setContig(EntryType.Contig value) {
- this.contig = value;
- }
+ protected List<EntryType.Feature.Qualifier> qualifier;
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequence() {
- return sequence;
- }
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequence(String value) {
- this.sequence = value;
- }
+ @XmlAttribute(name = "location", required = true)
+ protected String location;
/**
- * Gets the value of the accession property.
+ * Gets the value of the taxon property.
+ *
+ * @return possible object is {@link EntryType.Feature.FeatureTaxon }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getAccession() {
- return accession;
+ public EntryType.Feature.FeatureTaxon getTaxon()
+ {
+ return taxon;
}
/**
- * Sets the value of the accession property.
+ * Sets the value of the taxon property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccession(String value) {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
+ * allowed object is {@link EntryType.Feature.FeatureTaxon }
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getVersion() {
- return version;
+ public void setTaxon(EntryType.Feature.FeatureTaxon value)
+ {
+ this.taxon = value;
}
/**
- * Sets the value of the version property.
+ * Gets the value of the xref property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the entryVersion 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 xref property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEntryVersion() {
- return entryVersion;
- }
-
- /**
- * Sets the value of the entryVersion property.
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEntryVersion(BigInteger value) {
- this.entryVersion = value;
- }
-
- /**
- * Gets the value of the dataClass property.
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDataClass() {
- return dataClass;
- }
-
- /**
- * Sets the value of the dataClass property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDataClass(String value) {
- this.dataClass = value;
- }
-
- /**
- * Gets the value of the taxonomicDivision property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link XrefType
+ * }
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTaxonomicDivision() {
- return taxonomicDivision;
- }
-
- /**
- * Sets the value of the taxonomicDivision property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setTaxonomicDivision(String value) {
- this.taxonomicDivision = value;
+ public List<XrefType> getXref()
+ {
+ if (xref == null)
+ {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
}
/**
- * Gets the value of the moleculeType property.
+ * Gets the value of the qualifier property.
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMoleculeType() {
- return moleculeType;
- }
-
- /**
- * Sets the value of the moleculeType 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 qualifier property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMoleculeType(String value) {
- this.moleculeType = value;
- }
-
- /**
- * Gets the value of the sequenceLength property.
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getSequenceLength() {
- return sequenceLength;
- }
-
- /**
- * Sets the value of the sequenceLength property.
+ * <pre>
+ * getQualifier().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setSequenceLength(BigInteger value) {
- this.sequenceLength = value;
- }
-
- /**
- * Gets the value of the topology property.
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTopology() {
- return topology;
- }
-
- /**
- * Sets the value of the topology property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.Qualifier }
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTopology(String value) {
- this.topology = value;
- }
-
- /**
- * Gets the value of the firstPublic property.
*
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
*/
- public XMLGregorianCalendar getFirstPublic() {
- return firstPublic;
+ public List<EntryType.Feature.Qualifier> getQualifier()
+ {
+ if (qualifier == null)
+ {
+ qualifier = new ArrayList<EntryType.Feature.Qualifier>();
+ }
+ return this.qualifier;
}
/**
- * Sets the value of the firstPublic property.
+ * Gets the value of the name property.
*
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setFirstPublic(XMLGregorianCalendar value) {
- this.firstPublic = value;
- }
-
- /**
- * Gets the value of the firstPublicRelease property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getFirstPublicRelease() {
- return firstPublicRelease;
+ public String getName()
+ {
+ return name;
}
/**
- * Sets the value of the firstPublicRelease property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setFirstPublicRelease(BigInteger value) {
- this.firstPublicRelease = value;
- }
-
- /**
- * Gets the value of the lastUpdated property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
*/
- public XMLGregorianCalendar getLastUpdated() {
- return lastUpdated;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Sets the value of the lastUpdated property.
+ * Gets the value of the location property.
*
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setLastUpdated(XMLGregorianCalendar value) {
- this.lastUpdated = value;
- }
-
- /**
- * Gets the value of the lastUpdatedRelease property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getLastUpdatedRelease() {
- return lastUpdatedRelease;
+ public String getLocation()
+ {
+ return location;
}
/**
- * Sets the value of the lastUpdatedRelease property.
+ * Sets the value of the location property.
*
* @param value
- * allowed object is
- * {@link BigInteger }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setLastUpdatedRelease(BigInteger value) {
- this.lastUpdatedRelease = value;
+ public void setLocation(String value)
+ {
+ this.location = value;
}
-
/**
- * <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="range" maxOccurs="unbounded">
+ * <element name="lineage" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "range"
- })
- public static class Assembly {
+ @XmlType(name = "", propOrder = { "lineage" })
+ public static class FeatureTaxon
+ {
+
+ protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+
+ @XmlAttribute(name = "commonName")
+ protected String commonName;
+
+ @XmlAttribute(name = "taxId")
+ protected BigInteger taxId;
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return possible object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage getLineage()
+ {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value)
+ {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScientificName()
+ {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScientificName(String value)
+ {
+ this.scientificName = value;
+ }
+
+ /**
+ * Gets the value of the commonName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCommonName()
+ {
+ return commonName;
+ }
+
+ /**
+ * Sets the value of the commonName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCommonName(String value)
+ {
+ this.commonName = value;
+ }
+
+ /**
+ * Gets the value of the taxId property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getTaxId()
+ {
+ return taxId;
+ }
+
+ /**
+ * Sets the value of the taxId property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setTaxId(BigInteger value)
+ {
+ this.taxId = 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="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "taxon" })
+ public static class Lineage
+ {
@XmlElement(required = true)
- protected List<EntryType.Assembly.Range> range;
+ protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
/**
- * Gets the value of the range property.
+ * Gets the value of the taxon 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 range property.
+ * 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 taxon property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getRange().add(newItem);
+ * getTaxon().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EntryType.Assembly.Range }
- *
- *
- */
- public List<EntryType.Assembly.Range> getRange() {
- if (range == null) {
- range = new ArrayList<EntryType.Assembly.Range>();
- }
- return this.range;
- }
-
-
- /**
- * <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="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Range {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
- @XmlAttribute(name = "primaryBegin")
- protected BigInteger primaryBegin;
- @XmlAttribute(name = "primaryEnd")
- protected BigInteger primaryEnd;
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
- @XmlAttribute(name = "complement")
- protected Boolean complement;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the primaryBegin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryBegin() {
- return primaryBegin;
- }
-
- /**
- * Sets the value of the primaryBegin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryBegin(BigInteger value) {
- this.primaryBegin = value;
- }
-
- /**
- * Gets the value of the primaryEnd property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryEnd() {
- return primaryEnd;
- }
-
- /**
- * Sets the value of the primaryEnd property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryEnd(BigInteger value) {
- this.primaryEnd = value;
- }
-
- /**
- * Gets the value of the accession property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAccession() {
- return accession;
- }
-
- /**
- * Sets the value of the accession property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccession(String value) {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the complement property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isComplement() {
- if (complement == null) {
- return false;
- } else {
- return complement;
- }
- }
-
- /**
- * Sets the value of the complement property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setComplement(Boolean value) {
- this.complement = value;
- }
-
+ public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon()
+ {
+ if (taxon == null)
+ {
+ taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
+ }
+ return this.taxon;
}
- }
-
-
- /**
- * <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>
- * <choice maxOccurs="unbounded" minOccurs="0">
- * <element name="range">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="gap">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </choice>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "rangeOrGap"
- })
- public static class Contig {
-
- @XmlElements({
- @XmlElement(name = "range", type = EntryType.Contig.Range.class),
- @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
- })
- protected List<Object> rangeOrGap;
-
/**
- * Gets the value of the rangeOrGap 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 rangeOrGap property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getRangeOrGap().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Contig.Range }
- * {@link EntryType.Contig.Gap }
- *
- *
- */
- public List<Object> getRangeOrGap() {
- if (rangeOrGap == null) {
- rangeOrGap = new ArrayList<Object>();
- }
- return this.rangeOrGap;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * 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="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "")
- public static class Gap {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
- @XmlAttribute(name = "length", required = true)
- protected BigInteger length;
- @XmlAttribute(name = "unknownLength")
- protected Boolean unknownLength;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the length property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getLength() {
- return length;
- }
-
- /**
- * Sets the value of the length property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setLength(BigInteger value) {
- this.length = value;
- }
-
- /**
- * Gets the value of the unknownLength property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isUnknownLength() {
- if (unknownLength == null) {
- return false;
- } else {
- return unknownLength;
- }
- }
-
- /**
- * Sets the value of the unknownLength property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setUnknownLength(Boolean value) {
- this.unknownLength = value;
- }
+ public static class Taxon
+ {
+
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScientificName()
+ {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScientificName(String value)
+ {
+ this.scientificName = 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="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Range {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
- @XmlAttribute(name = "primaryBegin")
- protected BigInteger primaryBegin;
- @XmlAttribute(name = "primaryEnd")
- protected BigInteger primaryEnd;
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
- @XmlAttribute(name = "complement")
- protected Boolean complement;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the primaryBegin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryBegin() {
- return primaryBegin;
- }
-
- /**
- * Sets the value of the primaryBegin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryBegin(BigInteger value) {
- this.primaryBegin = value;
- }
-
- /**
- * Gets the value of the primaryEnd property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryEnd() {
- return primaryEnd;
- }
-
- /**
- * Sets the value of the primaryEnd property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryEnd(BigInteger value) {
- this.primaryEnd = value;
- }
-
- /**
- * Gets the value of the accession property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAccession() {
- return accession;
- }
-
- /**
- * Sets the value of the accession property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccession(String value) {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the complement property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isComplement() {
- if (complement == null) {
- return false;
- } else {
- return complement;
- }
- }
-
- /**
- * Sets the value of the complement property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setComplement(Boolean value) {
- this.complement = value;
- }
-
- }
+ }
}
-
/**
- * <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="taxon" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="lineage" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* </sequence>
* <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "taxon",
- "xref",
- "qualifier"
- })
- public static class Feature {
-
- protected EntryType.Feature.FeatureTaxon taxon;
- protected List<XrefType> xref;
- protected List<EntryType.Feature.Qualifier> qualifier;
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "location", required = true)
- protected String location;
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Qualifier
+ {
+
+ protected String value;
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * 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 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 taxon property.
- *
- * @return
- * possible object is
- * {@link EntryType.Feature.FeatureTaxon }
- *
- */
- public EntryType.Feature.FeatureTaxon getTaxon() {
- return taxon;
- }
+ }
- /**
- * Sets the value of the taxon property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Feature.FeatureTaxon }
- *
- */
- public void setTaxon(EntryType.Feature.FeatureTaxon value) {
- this.taxon = 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="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+ * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="submission"/>
+ * <enumeration value="book"/>
+ * <enumeration value="article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "title", "author", "applicant", "consortium", "submissionDate",
+ "journal", "year", "volume", "issue", "firstPage", "lastPage",
+ "comment", "referenceLocation", "xref" })
+ public static class Reference
+ {
+
+ protected String title;
+
+ protected List<String> author;
+
+ protected List<String> applicant;
+
+ protected String consortium;
- /**
- * Gets the value of the xref 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 xref property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getXref().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link XrefType }
- *
- *
- */
- public List<XrefType> getXref() {
- if (xref == null) {
- xref = new ArrayList<XrefType>();
- }
- return this.xref;
- }
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar submissionDate;
- /**
- * Gets the value of the qualifier 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 qualifier property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getQualifier().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature.Qualifier }
- *
- *
- */
- public List<EntryType.Feature.Qualifier> getQualifier() {
- if (qualifier == null) {
- qualifier = new ArrayList<EntryType.Feature.Qualifier>();
- }
- return this.qualifier;
- }
+ protected String journal;
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ protected String year;
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ protected String volume;
- /**
- * Gets the value of the location property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLocation() {
- return location;
- }
+ protected String issue;
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocation(String value) {
- this.location = value;
- }
+ protected String firstPage;
+ protected String lastPage;
- /**
- * <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="lineage" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "lineage"
- })
- public static class FeatureTaxon {
-
- protected EntryType.Feature.FeatureTaxon.Lineage lineage;
- @XmlAttribute(name = "scientificName", required = true)
- protected String scientificName;
- @XmlAttribute(name = "commonName")
- protected String commonName;
- @XmlAttribute(name = "taxId")
- protected BigInteger taxId;
-
- /**
- * Gets the value of the lineage property.
- *
- * @return
- * possible object is
- * {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
- return lineage;
- }
-
- /**
- * Sets the value of the lineage property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
- this.lineage = value;
- }
-
- /**
- * Gets the value of the scientificName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScientificName() {
- return scientificName;
- }
-
- /**
- * Sets the value of the scientificName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScientificName(String value) {
- this.scientificName = value;
- }
-
- /**
- * Gets the value of the commonName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * Sets the value of the commonName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCommonName(String value) {
- this.commonName = value;
- }
-
- /**
- * Gets the value of the taxId property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getTaxId() {
- return taxId;
- }
-
- /**
- * Sets the value of the taxId property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setTaxId(BigInteger value) {
- this.taxId = 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="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "taxon"
- })
- public static class Lineage {
-
- @XmlElement(required = true)
- protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
-
- /**
- * Gets the value of the taxon 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 taxon property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTaxon().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
- *
- *
- */
- public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon() {
- if (taxon == null) {
- taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
- }
- return this.taxon;
- }
-
-
- /**
- * <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="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Taxon {
-
- @XmlAttribute(name = "scientificName", required = true)
- protected String scientificName;
-
- /**
- * Gets the value of the scientificName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScientificName() {
- return scientificName;
- }
-
- /**
- * Sets the value of the scientificName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScientificName(String value) {
- this.scientificName = value;
- }
-
- }
-
- }
+ protected String comment;
- }
+ protected String referenceLocation;
+ protected List<XrefType> xref;
- /**
- * <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="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Qualifier {
-
- protected String value;
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * 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 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;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- }
+ @XmlAttribute(name = "number", required = true)
+ protected BigInteger number;
+
+ @XmlAttribute(name = "location")
+ protected String location;
+ /**
+ * 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.
+ * Gets the value of the author property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 author property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
- * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="submission"/>
- * <enumeration value="book"/>
- * <enumeration value="article"/>
- * <enumeration value="patent"/>
- * <enumeration value="thesis"/>
- * <enumeration value="unpublished"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getAuthor().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "author",
- "applicant",
- "consortium",
- "submissionDate",
- "journal",
- "year",
- "volume",
- "issue",
- "firstPage",
- "lastPage",
- "comment",
- "referenceLocation",
- "xref"
- })
- public static class Reference {
-
- protected String title;
- protected List<String> author;
- protected List<String> applicant;
- protected String consortium;
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar submissionDate;
- protected String journal;
- protected String year;
- protected String volume;
- protected String issue;
- protected String firstPage;
- protected String lastPage;
- protected String comment;
- protected String referenceLocation;
- protected List<XrefType> xref;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "number", required = true)
- protected BigInteger number;
- @XmlAttribute(name = "location")
- protected String location;
-
- /**
- * 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;
- }
+ public List<String> getAuthor()
+ {
+ if (author == null)
+ {
+ author = new ArrayList<String>();
+ }
+ return this.author;
+ }
- /**
- * Gets the value of the author 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 author property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAuthor().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAuthor() {
- if (author == null) {
- author = new ArrayList<String>();
- }
- return this.author;
- }
-
- /**
- * Gets the value of the applicant 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 applicant property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getApplicant().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getApplicant() {
- if (applicant == null) {
- applicant = new ArrayList<String>();
- }
- return this.applicant;
- }
-
- /**
- * Gets the value of the consortium property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getConsortium() {
- return consortium;
- }
+ /**
+ * Gets the value of the applicant 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 applicant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getApplicant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getApplicant()
+ {
+ if (applicant == null)
+ {
+ applicant = new ArrayList<String>();
+ }
+ return this.applicant;
+ }
- /**
- * Sets the value of the consortium property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setConsortium(String value) {
- this.consortium = value;
- }
+ /**
+ * Gets the value of the consortium property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getConsortium()
+ {
+ return consortium;
+ }
- /**
- * Gets the value of the submissionDate property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getSubmissionDate() {
- return submissionDate;
- }
+ /**
+ * Sets the value of the consortium property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setConsortium(String value)
+ {
+ this.consortium = value;
+ }
- /**
- * Sets the value of the submissionDate property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setSubmissionDate(XMLGregorianCalendar value) {
- this.submissionDate = value;
- }
+ /**
+ * Gets the value of the submissionDate property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getSubmissionDate()
+ {
+ return submissionDate;
+ }
- /**
- * Gets the value of the journal property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getJournal() {
- return journal;
- }
+ /**
+ * Sets the value of the submissionDate property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setSubmissionDate(XMLGregorianCalendar value)
+ {
+ this.submissionDate = value;
+ }
- /**
- * Sets the value of the journal property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setJournal(String value) {
- this.journal = value;
- }
+ /**
+ * Gets the value of the journal property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getJournal()
+ {
+ return journal;
+ }
- /**
- * Gets the value of the year property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getYear() {
- return year;
- }
+ /**
+ * Sets the value of the journal property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setJournal(String value)
+ {
+ this.journal = value;
+ }
- /**
- * Sets the value of the year property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setYear(String value) {
- this.year = value;
- }
+ /**
+ * Gets the value of the year property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getYear()
+ {
+ return year;
+ }
- /**
- * Gets the value of the volume property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVolume() {
- return volume;
- }
+ /**
+ * Sets the value of the year property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setYear(String value)
+ {
+ this.year = value;
+ }
- /**
- * Sets the value of the volume property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVolume(String value) {
- this.volume = value;
- }
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVolume()
+ {
+ return volume;
+ }
- /**
- * Gets the value of the issue property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getIssue() {
- return issue;
- }
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVolume(String value)
+ {
+ this.volume = value;
+ }
- /**
- * Sets the value of the issue property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setIssue(String value) {
- this.issue = value;
- }
+ /**
+ * Gets the value of the issue property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getIssue()
+ {
+ return issue;
+ }
- /**
- * Gets the value of the firstPage property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFirstPage() {
- return firstPage;
- }
+ /**
+ * Sets the value of the issue property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setIssue(String value)
+ {
+ this.issue = value;
+ }
- /**
- * Sets the value of the firstPage property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFirstPage(String value) {
- this.firstPage = value;
- }
+ /**
+ * Gets the value of the firstPage property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFirstPage()
+ {
+ return firstPage;
+ }
- /**
- * Gets the value of the lastPage property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLastPage() {
- return lastPage;
- }
+ /**
+ * Sets the value of the firstPage property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFirstPage(String value)
+ {
+ this.firstPage = value;
+ }
- /**
- * Sets the value of the lastPage property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLastPage(String value) {
- this.lastPage = value;
- }
+ /**
+ * Gets the value of the lastPage property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLastPage()
+ {
+ return lastPage;
+ }
- /**
- * Gets the value of the comment property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComment() {
- return comment;
- }
+ /**
+ * Sets the value of the lastPage property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLastPage(String value)
+ {
+ this.lastPage = value;
+ }
- /**
- * Sets the value of the comment property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setComment(String value) {
- this.comment = value;
- }
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComment()
+ {
+ return comment;
+ }
- /**
- * Gets the value of the referenceLocation property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getReferenceLocation() {
- return referenceLocation;
- }
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComment(String value)
+ {
+ this.comment = value;
+ }
- /**
- * Sets the value of the referenceLocation property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setReferenceLocation(String value) {
- this.referenceLocation = value;
- }
+ /**
+ * Gets the value of the referenceLocation property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getReferenceLocation()
+ {
+ return referenceLocation;
+ }
- /**
- * Gets the value of the xref 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 xref property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getXref().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link XrefType }
- *
- *
- */
- public List<XrefType> getXref() {
- if (xref == null) {
- xref = new ArrayList<XrefType>();
- }
- return this.xref;
- }
+ /**
+ * Sets the value of the referenceLocation property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setReferenceLocation(String value)
+ {
+ this.referenceLocation = value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * Gets the value of the xref 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 xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link XrefType
+ * }
+ *
+ *
+ */
+ public List<XrefType> getXref()
+ {
+ if (xref == null)
+ {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
- /**
- * 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 type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Gets the value of the number property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getNumber() {
- return number;
- }
+ /**
+ * 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 number property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setNumber(BigInteger value) {
- this.number = value;
- }
+ /**
+ * Gets the value of the number property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getNumber()
+ {
+ return number;
+ }
- /**
- * Gets the value of the location property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLocation() {
- return location;
- }
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setNumber(BigInteger value)
+ {
+ this.number = value;
+ }
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocation(String value) {
- this.location = value;
- }
+ /**
+ * Gets the value of the location property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLocation()
+ {
+ return location;
+ }
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLocation(String value)
+ {
+ this.location = value;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlRegistry;
-
/**
- * This object contains factory methods for each
- * Java content interface and Java element interface
- * generated in the jalview.xml.binding.embl 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.embl 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 {
-
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link EntryType }
- *
- */
- public EntryType createEntryType() {
- return new EntryType();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig }
- *
- */
- public EntryType.Contig createEntryTypeContig() {
- return new EntryType.Contig();
- }
-
- /**
- * Create an instance of {@link EntryType.Assembly }
- *
- */
- public EntryType.Assembly createEntryTypeAssembly() {
- return new EntryType.Assembly();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature }
- *
- */
- public EntryType.Feature createEntryTypeFeature() {
- return new EntryType.Feature();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon }
- *
- */
- public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
- return new EntryType.Feature.FeatureTaxon();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
- return new EntryType.Feature.FeatureTaxon.Lineage();
- }
-
- /**
- * Create an instance of {@link ROOT }
- *
- */
- public ROOT createROOT() {
- return new ROOT();
- }
-
- /**
- * Create an instance of {@link EntrySetType }
- *
- */
- public EntrySetType createEntrySetType() {
- return new EntrySetType();
- }
-
- /**
- * Create an instance of {@link XrefType }
- *
- */
- public XrefType createXrefType() {
- return new XrefType();
- }
-
- /**
- * Create an instance of {@link EntryType.Reference }
- *
- */
- public EntryType.Reference createEntryTypeReference() {
- return new EntryType.Reference();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig.Range }
- *
- */
- public EntryType.Contig.Range createEntryTypeContigRange() {
- return new EntryType.Contig.Range();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig.Gap }
- *
- */
- public EntryType.Contig.Gap createEntryTypeContigGap() {
- return new EntryType.Contig.Gap();
- }
-
- /**
- * Create an instance of {@link EntryType.Assembly.Range }
- *
- */
- public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
- return new EntryType.Assembly.Range();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.Qualifier }
- *
- */
- public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
- return new EntryType.Feature.Qualifier();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
- return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
- }
+public class ObjectFactory
+{
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.embl
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link EntryType }
+ *
+ */
+ public EntryType createEntryType()
+ {
+ return new EntryType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig createEntryTypeContig()
+ {
+ return new EntryType.Contig();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly createEntryTypeAssembly()
+ {
+ return new EntryType.Assembly();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature }
+ *
+ */
+ public EntryType.Feature createEntryTypeFeature()
+ {
+ return new EntryType.Feature();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon()
+ {
+ return new EntryType.Feature.FeatureTaxon();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage()
+ {
+ return new EntryType.Feature.FeatureTaxon.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ROOT }
+ *
+ */
+ public ROOT createROOT()
+ {
+ return new ROOT();
+ }
+
+ /**
+ * Create an instance of {@link EntrySetType }
+ *
+ */
+ public EntrySetType createEntrySetType()
+ {
+ return new EntrySetType();
+ }
+
+ /**
+ * Create an instance of {@link XrefType }
+ *
+ */
+ public XrefType createXrefType()
+ {
+ return new XrefType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Reference }
+ *
+ */
+ public EntryType.Reference createEntryTypeReference()
+ {
+ return new EntryType.Reference();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Range }
+ *
+ */
+ public EntryType.Contig.Range createEntryTypeContigRange()
+ {
+ return new EntryType.Contig.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Gap }
+ *
+ */
+ public EntryType.Contig.Gap createEntryTypeContigGap()
+ {
+ return new EntryType.Contig.Gap();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly.Range }
+ *
+ */
+ public EntryType.Assembly.Range createEntryTypeAssemblyRange()
+ {
+ return new EntryType.Assembly.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.Qualifier }
+ *
+ */
+ public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier()
+ {
+ return new EntryType.Feature.Qualifier();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon()
+ {
+ return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.embl;
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>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "entrySet",
- "entry"
-})
+@XmlType(name = "", propOrder = { "entrySet", "entry" })
@XmlRootElement(name = "ROOT")
-public class ROOT {
+public class ROOT
+{
+
+ protected EntrySetType entrySet;
- protected EntrySetType entrySet;
- protected EntryType entry;
+ protected EntryType entry;
- /**
- * Gets the value of the entrySet property.
- *
- * @return
- * possible object is
- * {@link EntrySetType }
- *
- */
- public EntrySetType getEntrySet() {
- return entrySet;
- }
+ /**
+ * Gets the value of the entrySet property.
+ *
+ * @return possible object is {@link EntrySetType }
+ *
+ */
+ public EntrySetType getEntrySet()
+ {
+ return entrySet;
+ }
- /**
- * Sets the value of the entrySet property.
- *
- * @param value
- * allowed object is
- * {@link EntrySetType }
- *
- */
- public void setEntrySet(EntrySetType value) {
- this.entrySet = value;
- }
+ /**
+ * Sets the value of the entrySet property.
+ *
+ * @param value
+ * allowed object is {@link EntrySetType }
+ *
+ */
+ public void setEntrySet(EntrySetType value)
+ {
+ this.entrySet = value;
+ }
- /**
- * Gets the value of the entry property.
- *
- * @return
- * possible object is
- * {@link EntryType }
- *
- */
- public EntryType getEntry() {
- return entry;
- }
+ /**
+ * Gets the value of the entry property.
+ *
+ * @return possible object is {@link EntryType }
+ *
+ */
+ public EntryType getEntry()
+ {
+ return entry;
+ }
- /**
- * Sets the value of the entry property.
- *
- * @param value
- * allowed object is
- * {@link EntryType }
- *
- */
- public void setEntry(EntryType value) {
- this.entry = value;
- }
+ /**
+ * Sets the value of the entry property.
+ *
+ * @param value
+ * allowed object is {@link EntryType }
+ *
+ */
+ public void setEntry(EntryType value)
+ {
+ this.entry = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
* Database cross-reference.
*
- * <p>Java class for XrefType complex type.
+ * <p>
+ * Java class for XrefType 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="XrefType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "XrefType")
-public class XrefType {
+public class XrefType
+{
+
+ @XmlAttribute(name = "db", required = true)
+ protected String db;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- @XmlAttribute(name = "db", required = true)
- protected String db;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "secondaryId")
- protected String secondaryId;
+ @XmlAttribute(name = "secondaryId")
+ protected String secondaryId;
- /**
- * Gets the value of the db property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDb() {
- return db;
- }
+ /**
+ * Gets the value of the db property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDb()
+ {
+ return db;
+ }
- /**
- * Sets the value of the db property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDb(String value) {
- this.db = value;
- }
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDb(String value)
+ {
+ this.db = 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 secondaryId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSecondaryId() {
- return secondaryId;
- }
+ /**
+ * Gets the value of the secondaryId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSecondaryId()
+ {
+ return secondaryId;
+ }
- /**
- * Sets the value of the secondaryId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSecondaryId(String value) {
- this.secondaryId = value;
- }
+ /**
+ * Sets the value of the secondaryId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSecondaryId(String value)
+ {
+ this.secondaryId = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "alcodon",
- "alcodMap"
-})
+@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
@XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame {
+public class AlcodonFrame
+{
+
+ protected List<AlcodonFrame.Alcodon> alcodon;
+
+ protected List<AlcodonFrame.AlcodMap> alcodMap;
- protected List<AlcodonFrame.Alcodon> alcodon;
- protected List<AlcodonFrame.AlcodMap> alcodMap;
+ /**
+ * 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;
/**
- * 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.
+ * a Mapping entry and an associated protein sequence
*
- * <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 }
*
+ * @return possible object is {@link Mapping }
*
*/
- public List<AlcodonFrame.Alcodon> getAlcodon() {
- if (alcodon == null) {
- alcodon = new ArrayList<AlcodonFrame.Alcodon>();
- }
- return this.alcodon;
+ public Mapping getMapping()
+ {
+ return mapping;
}
/**
- * 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 }
+ * Sets the value of the mapping property.
*
+ * @param value
+ * allowed object is {@link Mapping }
*
*/
- public List<AlcodonFrame.AlcodMap> getAlcodMap() {
- if (alcodMap == null) {
- alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
- }
- return this.alcodMap;
+ public void setMapping(Mapping value)
+ {
+ this.mapping = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the dnasq property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <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>
+ */
+ public String getDnasq()
+ {
+ return dnasq;
+ }
+
+ /**
+ * Sets the value of the dnasq property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "mapping"
- })
- public static class AlcodMap {
+ public void setDnasq(String value)
+ {
+ this.dnasq = value;
+ }
- @XmlElement(name = "Mapping", required = true)
- protected Mapping mapping;
- @XmlAttribute(name = "dnasq", required = true)
- protected String dnasq;
+ }
- /**
- *
- * a Mapping entry and an associated protein sequence
- *
- *
- * @return
- * possible object is
- * {@link Mapping }
- *
- */
- public Mapping getMapping() {
- return mapping;
- }
+ /**
+ *
+ * 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
+ {
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link Mapping }
- *
- */
- public void setMapping(Mapping value) {
- this.mapping = value;
- }
+ @XmlAttribute(name = "pos1")
+ protected BigInteger pos1;
- /**
- * Gets the value of the dnasq property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDnasq() {
- return dnasq;
- }
+ @XmlAttribute(name = "pos2")
+ protected BigInteger pos2;
- /**
- * Sets the value of the dnasq property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDnasq(String value) {
- this.dnasq = value;
- }
+ @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.
*
- * 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).
- *
+ * @param value
+ * allowed object is {@link BigInteger }
*
- * <p>Java class for anonymous complex type.
+ */
+ public void setPos1(BigInteger value)
+ {
+ this.pos1 = value;
+ }
+
+ /**
+ * Gets the value of the pos2 property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link BigInteger }
*
- * <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>
+ */
+ public BigInteger getPos2()
+ {
+ return pos2;
+ }
+
+ /**
+ * Sets the value of the pos2 property.
*
+ * @param value
+ * allowed object is {@link BigInteger }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Alcodon {
-
- @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;
- }
+ public void setPos2(BigInteger value)
+ {
+ this.pos2 = value;
+ }
- /**
- * Sets the value of the pos3 property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPos3(BigInteger value) {
- this.pos3 = 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;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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>
*
*/
@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 {
-
- protected List<AnnotationElement> annotationElement;
- @XmlElement(required = true)
- protected String label;
- protected String description;
- 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;
- }
+public class Annotation
+{
- /**
- * 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;
- }
+ protected List<AnnotationElement> annotationElement;
- /**
- * Sets the value of the groupRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGroupRef(String value) {
- this.groupRef = value;
- }
+ @XmlElement(required = true)
+ protected String label;
+
+ protected String description;
- /**
- * 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;
- }
+ 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;
- /**
- * Sets the value of the score property.
- *
- * @param value
- * allowed object is
- * {@link Double }
- *
- */
- public void setScore(Double value) {
- this.score = value;
- }
+ @XmlAttribute(name = "value")
+ protected Float value;
- /**
- * Gets the value of the visible property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isVisible() {
- return visible;
- }
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
/**
- * Sets the value of the visible property.
+ * Gets the value of the label 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 String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isCentreColLabels() {
- return centreColLabels;
+ public String getLabel()
+ {
+ return label;
}
/**
- * Sets the value of the centreColLabels property.
+ * Sets the value of the label property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCentreColLabels(Boolean value) {
- this.centreColLabels = value;
- }
-
- /**
- * Gets the value of the scaleColLabels property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isScaleColLabels() {
- return scaleColLabels;
+ public void setLabel(String value)
+ {
+ this.label = value;
}
/**
- * Sets the value of the scaleColLabels property.
+ * Gets the value of the value 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 Float }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowAllColLabels() {
- return showAllColLabels;
+ public Float getValue()
+ {
+ return value;
}
/**
- * Sets the value of the showAllColLabels property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAllColLabels(Boolean value) {
- this.showAllColLabels = value;
- }
-
- /**
- * Gets the value of the autoCalculated property.
+ * allowed object is {@link Float }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isAutoCalculated() {
- if (autoCalculated == null) {
- return false;
- } else {
- return autoCalculated;
- }
+ public void setValue(Float value)
+ {
+ this.value = value;
}
/**
- * Sets the value of the autoCalculated property.
+ * Gets the value of the colour 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 Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isBelowAlignment() {
- if (belowAlignment == null) {
- return true;
- } else {
- return belowAlignment;
- }
+ public Integer getColour()
+ {
+ return colour;
}
/**
- * Sets the value of the belowAlignment property.
+ * Sets the value of the colour property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setBelowAlignment(Boolean value) {
- this.belowAlignment = value;
- }
-
- /**
- * Gets the value of the calcId property.
+ * allowed object is {@link Integer }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getCalcId() {
- return calcId;
+ public void setColour(Integer value)
+ {
+ this.colour = value;
}
- /**
- * 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;
- @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;
- }
-
- }
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*/
@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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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>
*
*/
@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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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>();
- }
- 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;
+@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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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>();
- }
- return this.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>();
}
+ return this.v;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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>();
- }
- return this.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;
+ }
+
+ /**
+ * 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 begin property.
+ * Gets the value of the key 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 }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public String getKey()
+ {
+ return key;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the key property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the description property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDescription() {
- return description;
+ public void setKey(String value)
+ {
+ this.key = value;
}
/**
- * Sets the value of the description property.
+ * Gets the value of the key2 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 }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getStatus() {
- return status;
+ public String getKey2()
+ {
+ return key2;
}
/**
- * Sets the value of the status property.
+ * Sets the value of the key2 property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
- /**
- * Gets the value of the featureGroup property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getFeatureGroup() {
- return featureGroup;
+ public void setKey2(String value)
+ {
+ this.key2 = value;
}
/**
- * Sets the value of the featureGroup property.
+ * Gets the value of the value 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 String }
*
- * @return
- * possible object is
- * {@link Float }
- *
*/
- public Float getScore() {
- return score;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the score property.
+ * Sets the value of the value 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>
- *
+ * allowed object is {@link String }
*
*/
- @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;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
- "attributeName",
- "condition",
- "value"
-})
-public class FeatureMatcher {
+@XmlType(
+ name = "FeatureMatcher",
+ namespace = "www.jalview.org/colours",
+ propOrder =
+ { "attributeName", "condition", "value" })
+public class FeatureMatcher
+{
- @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 = "")
+ protected List<String> attributeName;
- /**
- * 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;
- }
+ @XmlElement(namespace = "", required = true)
+ protected String condition;
- /**
- * Gets the value of the condition property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCondition() {
- return condition;
- }
+ @XmlElement(namespace = "", required = true)
+ protected String value;
- /**
- * Sets the value of the condition property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCondition(String value) {
- this.condition = value;
- }
+ @XmlAttribute(name = "by")
+ protected FilterBy by;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
+ /**
+ * 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;
+ }
- /**
- * 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 condition property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCondition()
+ {
+ return condition;
+ }
- /**
- * Gets the value of the by property.
- *
- * @return
- * possible object is
- * {@link FilterBy }
- *
- */
- public FilterBy getBy() {
- return by;
- }
+ /**
+ * 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 by property.
- *
- * @param value
- * allowed object is
- * {@link FilterBy }
- *
- */
- public void setBy(FilterBy value) {
- this.by = 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;
+ }
+
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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;
+@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;
/**
- * Gets the value of the matchCondition property.
+ * Gets the value of the matcherSet property.
*
- * @return
- * possible object is
- * {@link FeatureMatcher }
- *
- */
- public FeatureMatcher getMatchCondition() {
- return matchCondition;
- }
-
- /**
- * Sets the value of the matchCondition 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 }
*
- * @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;
+ public List<FeatureMatcherSet> getMatcherSet()
+ {
+ if (matcherSet == null)
+ {
+ matcherSet = new ArrayList<FeatureMatcherSet>();
+ }
+ return this.matcherSet;
}
/**
- * Sets the value of the compoundMatcher property.
+ * Gets the value of the and property.
*
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet.CompoundMatcher }
- *
*/
- public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
- this.compoundMatcher = value;
+ public boolean isAnd()
+ {
+ return and;
}
-
/**
- * <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>
- *
+ * Sets the value of the and property.
*
*/
- @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;
- }
-
+ public void setAnd(boolean value)
+ {
+ this.and = value;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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>
+ * 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">
*/
@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
+{
- public String value() {
- return value;
- }
+ @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 static FilterBy fromValue(String v) {
- for (FilterBy c: FilterBy.values()) {
- if (c.value.equals(v)) {
- return c;
- }
- }
- throw new IllegalArgumentException(v);
+ public static FilterBy fromValue(String v)
+ {
+ for (FilterBy c : FilterBy.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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;
+@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>();
}
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
+ 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>();
}
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
+ 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>();
}
-
- /**
- * Gets the value of the vamsasModel property.
- *
- * @return
- * possible object is
- * {@link VAMSAS }
- *
- */
- public VAMSAS getVamsasModel() {
- return vamsasModel;
+ 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>();
}
-
- /**
- * Sets the value of the vamsasModel property.
- *
- * @param value
- * allowed object is
- * {@link VAMSAS }
- *
- */
- public void setVamsasModel(VAMSAS value) {
- this.vamsasModel = value;
+ 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 jSeq property.
+ * 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 jSeq property.
+ * 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>
- * getJSeq().add(newItem);
+ * getSetting().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
+ * {@link JalviewModel.FeatureSettings.Setting }
*
*
*/
- public List<JalviewModel.JSeq> getJSeq() {
- if (jSeq == null) {
- jSeq = new ArrayList<JalviewModel.JSeq>();
- }
- return this.jSeq;
+ public List<JalviewModel.FeatureSettings.Setting> getSetting()
+ {
+ if (setting == null)
+ {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
}
/**
- * Gets the value of the jGroup property.
+ * 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 jGroup property.
+ * 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>
- * getJGroup().add(newItem);
+ * getGroup().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JGroup }
+ * {@link JalviewModel.FeatureSettings.Group }
*
*
*/
- public List<JalviewModel.JGroup> getJGroup() {
- if (jGroup == null) {
- jGroup = new ArrayList<JalviewModel.JGroup>();
- }
- return this.jGroup;
+ public List<JalviewModel.FeatureSettings.Group> getGroup()
+ {
+ if (group == null)
+ {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
}
/**
- * 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.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getViewport().add(newItem);
+ * <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>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport }
+ * 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>
*
*
*/
- public List<JalviewModel.Viewport> getViewport() {
- if (viewport == null) {
- viewport = new ArrayList<JalviewModel.Viewport>();
+ @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;
}
- return this.viewport;
+ 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 userColours 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 userColours property.
+ * 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>
- * getUserColours().add(newItem);
+ * getSeq().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.UserColours }
+ * Objects of the following type(s) are allowed in the list {@link String }
*
*
*/
- public List<JalviewModel.UserColours> getUserColours() {
- if (userColours == null) {
- userColours = new ArrayList<JalviewModel.UserColours>();
- }
- return this.userColours;
+ public List<String> getSeq()
+ {
+ if (seq == null)
+ {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
}
/**
- * Gets the value of the tree property.
+ * Gets the value of the annotationColours 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.
+ * @return possible object is {@link AnnotationColourScheme }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTree().add(newItem);
- * </pre>
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
*
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Tree }
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the start property.
*
+ * @return possible object is {@link Integer }
*
*/
- public List<JalviewModel.Tree> getTree() {
- if (tree == null) {
- tree = new ArrayList<JalviewModel.Tree>();
- }
- return this.tree;
+ public Integer getStart()
+ {
+ return start;
}
/**
- * Gets the value of the pcaViewer property.
+ * Sets the value of the start 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.
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getPcaViewer().add(newItem);
- * </pre>
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
*
+ * @return possible object is {@link Integer }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer }
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- public List<JalviewModel.PcaViewer> getPcaViewer() {
- if (pcaViewer == null) {
- pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
- }
- return this.pcaViewer;
+ public void setEnd(Integer value)
+ {
+ this.end = value;
}
/**
- * Gets the value of the featureSettings property.
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link JalviewModel.FeatureSettings }
- *
*/
- public JalviewModel.FeatureSettings getFeatureSettings() {
- return featureSettings;
+ public String getName()
+ {
+ return name;
}
/**
- * Sets the value of the featureSettings property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is
- * {@link JalviewModel.FeatureSettings }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setFeatureSettings(JalviewModel.FeatureSettings value) {
- this.featureSettings = value;
+ public void setName(String value)
+ {
+ this.name = value;
}
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColour()
+ {
+ return colour;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the colour property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link String }
*
- * <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>
+ */
+ public void setColour(String value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the consThreshold property.
*
+ * @return possible object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "setting",
- "group"
- })
- public static class FeatureSettings {
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Setting> setting;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Group> group;
+ /**
+ * 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 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 pidThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * 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;
- }
+ /**
+ * 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 outlineColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getOutlineColour()
+ {
+ return outlineColour;
+ }
- /**
- * <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;
- }
+ /**
+ * Sets the value of the outlineColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setOutlineColour(Integer value)
+ {
+ this.outlineColour = value;
+ }
- }
+ /**
+ * Gets the value of the displayBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDisplayBoxes()
+ {
+ return displayBoxes;
+ }
+ /**
+ * Sets the value of the displayBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDisplayBoxes(Boolean value)
+ {
+ this.displayBoxes = 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;
- }
+ /**
+ * Gets the value of the displayText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDisplayText()
+ {
+ return displayText;
+ }
- }
+ /**
+ * Sets the value of the displayText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDisplayText(Boolean value)
+ {
+ this.displayText = value;
+ }
+ /**
+ * Gets the value of the colourText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourText()
+ {
+ return colourText;
}
+ /**
+ * Sets the value of the colourText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourText(Boolean value)
+ {
+ this.colourText = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the textCol1 property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link Integer }
*
- * <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>
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
+
+ /**
+ * Sets the value of the textCol1 property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- @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;
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * 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 }
- *
- *
- */
- public List<String> getSeq() {
- if (seq == null) {
- seq = new ArrayList<String>();
- }
- return this.seq;
- }
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+ }
+
+ /**
+ * 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.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
+
+ /**
+ * 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 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;
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
/**
- * Sets the value of the annotationColours property.
+ * Gets the value of the value property.
*
- * @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 String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getStart() {
- return start;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the start property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getEnd() {
- return end;
+ public void setValue(String value)
+ {
+ this.value = value;
}
/**
- * Sets the value of the end property.
+ * Gets the value of the visible property.
*
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the name property.
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getName() {
- return name;
+ public Boolean isVisible()
+ {
+ return visible;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the visible property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the colour property.
+ * allowed object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getColour() {
- return colour;
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
}
/**
- * Sets the value of the colour property.
+ * Gets the value of the viewId property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColour(String value) {
- this.colour = value;
- }
-
- /**
- * Gets the value of the consThreshold property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getConsThreshold() {
- return consThreshold;
+ public String getViewId()
+ {
+ return viewId;
}
/**
- * Sets the value of the consThreshold property.
+ * Sets the value of the viewId property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
-
- /**
- * Gets the value of the pidThreshold property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getPidThreshold() {
- return pidThreshold;
+ public void setViewId(String value)
+ {
+ this.viewId = value;
}
/**
- * Sets the value of the pidThreshold property.
+ * Gets the value of the alignwithAlignPanel property.
*
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
-
- /**
- * Gets the value of the outlineColour property.
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getOutlineColour() {
- return outlineColour;
+ public boolean isAlignwithAlignPanel()
+ {
+ if (alignwithAlignPanel == null)
+ {
+ return true;
+ }
+ else
+ {
+ return alignwithAlignPanel;
+ }
}
/**
- * Sets the value of the outlineColour property.
+ * Sets the value of the alignwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setOutlineColour(Integer value) {
- this.outlineColour = value;
- }
-
- /**
- * Gets the value of the displayBoxes property.
+ * allowed object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayBoxes() {
- return displayBoxes;
+ public void setAlignwithAlignPanel(Boolean value)
+ {
+ this.alignwithAlignPanel = value;
}
/**
- * Sets the value of the displayBoxes property.
+ * Gets the value of the colourwithAlignPanel property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDisplayBoxes(Boolean value) {
- this.displayBoxes = value;
- }
-
- /**
- * Gets the value of the displayText property.
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayText() {
- return displayText;
+ public boolean isColourwithAlignPanel()
+ {
+ if (colourwithAlignPanel == null)
+ {
+ return false;
+ }
+ else
+ {
+ return colourwithAlignPanel;
+ }
}
/**
- * Sets the value of the displayText property.
+ * Sets the value of the colourwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setDisplayText(Boolean value) {
- this.displayText = value;
+ public void setColourwithAlignPanel(Boolean value)
+ {
+ this.colourwithAlignPanel = value;
}
/**
- * Gets the value of the colourText property.
+ * Gets the value of the colourByJmol property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isColourText() {
- return colourText;
+ public boolean isColourByJmol()
+ {
+ if (colourByJmol == null)
+ {
+ return true;
+ }
+ else
+ {
+ return colourByJmol;
+ }
}
/**
- * Sets the value of the colourText property.
+ * Sets the value of the colourByJmol property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setColourText(Boolean value) {
- this.colourText = value;
+ public void setColourByJmol(Boolean value)
+ {
+ this.colourByJmol = value;
}
/**
- * Gets the value of the textCol1 property.
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol1() {
- return textCol1;
+ public String getType()
+ {
+ return type;
}
/**
- * Sets the value of the textCol1 property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the textCol2 property.
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol2() {
- return textCol2;
+ public Integer getWidth()
+ {
+ return width;
}
/**
- * Sets the value of the textCol2 property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
+ public void setWidth(Integer value)
+ {
+ this.width = value;
}
/**
- * Gets the value of the textColThreshold property.
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextColThreshold() {
- return textColThreshold;
+ public Integer getHeight()
+ {
+ return height;
}
/**
- * Sets the value of the textColThreshold property.
+ * Sets the value of the height property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
+ public void setHeight(Integer value)
+ {
+ this.height = value;
}
/**
- * Gets the value of the showUnconserved property.
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowUnconserved() {
- return showUnconserved;
+ public Integer getXpos()
+ {
+ return xpos;
}
/**
- * Sets the value of the showUnconserved property.
+ * Sets the value of the xpos property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
}
/**
- * Gets the value of the ignoreGapsinConsensus property.
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
+ public Integer getYpos()
+ {
+ return ypos;
}
/**
- * Sets the value of the ignoreGapsinConsensus property.
+ * Sets the value of the ypos property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
+ 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">
+ * <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 showConsensusHistogram property.
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
+ public String getTitle()
+ {
+ return title;
}
/**
- * Sets the value of the showConsensusHistogram property.
+ * Sets the value of the title property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
+ public void setTitle(String value)
+ {
+ this.title = value;
}
/**
- * Gets the value of the showSequenceLogo property.
+ * Gets the value of the annotationId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
+ public String getAnnotationId()
+ {
+ return annotationId;
}
/**
- * Sets the value of the showSequenceLogo property.
+ * Sets the value of the annotationId property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
+ public void setAnnotationId(String value)
+ {
+ this.annotationId = value;
}
/**
- * Gets the value of the normaliseSequenceLogo property.
+ * Gets the value of the gapped property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
+ public Boolean isGapped()
+ {
+ return gapped;
}
/**
- * Sets the value of the normaliseSequenceLogo property.
+ * Sets the value of the gapped property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
+ public void setGapped(Boolean value)
+ {
+ this.gapped = value;
}
/**
- * Gets the value of the id property.
+ * Gets the value of the viewerState property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public String getViewerState()
+ {
+ return viewerState;
}
/**
- * Sets the value of the id property.
+ * Sets the value of the viewerState property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setId(String value) {
- this.id = value;
+ public void setViewerState(String value)
+ {
+ this.viewerState = 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 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;
+ }
+
+ /**
+ * 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 seqPointMin property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
+ {
+ return seqPointMin;
+ }
+
+ /**
+ * 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 seqPointMax property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
+ {
+ return seqPointMax;
+ }
+
+ /**
+ * 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 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;
+ }
+
+ /**
+ * 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 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;
+ }
+
+ /**
+ * 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;
}
+ /**
+ * Gets the value of the yDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYDim()
+ {
+ return yDim;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the yDim property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link Integer }
*
- * <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>
+ */
+ public void setYDim(Integer value)
+ {
+ this.yDim = value;
+ }
+
+ /**
+ * Gets the value of the zDim property.
*
+ * @return possible object is {@link Integer }
*
*/
- @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;
+ public Integer getZDim()
+ {
+ return zDim;
+ }
- /**
- * 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 zDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setZDim(Integer value)
+ {
+ this.zDim = 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 bgColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getBgColour()
+ {
+ return bgColour;
+ }
- /**
- * 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 bgColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value)
+ {
+ this.bgColour = 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 scaleFactor property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getScaleFactor()
+ {
+ return scaleFactor;
+ }
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
+ /**
+ * 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 colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
+ /**
+ * Gets the value of the showLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowLabels()
+ {
+ return showLabels;
+ }
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart() {
- return start;
- }
+ /**
+ * 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 start property.
- *
- */
- public void setStart(int value) {
- this.start = value;
- }
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews()
+ {
+ return linkToAllViews;
+ }
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
+ /**
+ * 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 end property.
- *
- */
- public void setEnd(int value) {
- this.end = value;
- }
+ /**
+ * Gets the value of the includeGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGaps()
+ {
+ return includeGaps;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * 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 id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps()
+ {
+ return matchGaps;
+ }
- /**
- * Gets the value of the hidden property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isHidden() {
- return hidden;
- }
+ /**
+ * 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 hidden property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setHidden(Boolean value) {
- this.hidden = value;
- }
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns()
+ {
+ return includeGappedColumns;
+ }
- /**
- * Gets the value of the viewreference property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isViewreference() {
- return viewreference;
- }
+ /**
+ * 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 viewreference property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setViewreference(Boolean value) {
- this.viewreference = 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;
+ }
- /**
- * <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
- {
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- @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;
-
- /**
- * 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 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;
+ }
- /**
- * <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 }
- *
- */
- 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 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>
+ * 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="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" />
+ * <attGroup ref="{www.jalview.org}position"/>
* </restriction>
* </complexContent>
* </complexType>
*
*/
@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 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;
- }
-
- /**
- * 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 seqPointMin property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
- return seqPointMin;
- }
-
- /**
- * 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 seqPointMax property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
- return seqPointMax;
- }
-
- /**
- * 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 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;
- }
-
- /**
- * 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 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;
- }
-
- /**
- * 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;
- }
-
- /**
- * Gets the value of the yDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYDim() {
- return yDim;
- }
+ @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 yDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYDim(Integer value) {
- this.yDim = value;
- }
+ }
- /**
- * Gets the value of the zDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getZDim() {
- return zDim;
- }
+ /**
+ * <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;
+ }
- /**
- * Sets the value of the zDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setZDim(Integer value) {
- this.zDim = value;
- }
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getBgColour() {
- return bgColour;
- }
+ /**
+ * <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;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setBgColour(Integer value) {
- this.bgColour = value;
- }
+ }
- /**
- * Gets the value of the scaleFactor property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getScaleFactor() {
- return scaleFactor;
- }
+ /**
+ * <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;
+ }
- /**
- * Sets the value of the scaleFactor property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setScaleFactor(Float value) {
- this.scaleFactor = value;
- }
+ }
- /**
- * Gets the value of the showLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowLabels() {
- return showLabels;
- }
+ }
+
+ /**
+ * <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;
- /**
- * Sets the value of the showLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowLabels(Boolean value) {
- this.showLabels = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isLinkToAllViews() {
- return linkToAllViews;
- }
+ /**
+ * 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 linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNewick()
+ {
+ return newick;
+ }
- /**
- * Gets the value of the includeGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGaps() {
- return includeGaps;
- }
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNewick(String value)
+ {
+ this.newick = value;
+ }
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the matchGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMatchGaps() {
- return matchGaps;
- }
+ /**
+ * 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 matchGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Gets the value of the includeGappedColumns property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
- }
+ /**
+ * 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 includeGappedColumns property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * Gets the value of the denominateByShortestLength property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
- }
+ /**
+ * 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 denominateByShortestLength property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = value;
- }
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = 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 showBootstrap property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap()
+ {
+ return showBootstrap;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value)
+ {
+ this.showBootstrap = 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 showDistances property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances()
+ {
+ return showDistances;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value)
+ {
+ this.showDistances = 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 markUnlinked property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked()
+ {
+ return markUnlinked;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value)
+ {
+ this.markUnlinked = value;
+ }
- /**
- * 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 fitToWindow property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow()
+ {
+ return fitToWindow;
+ }
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value)
+ {
+ this.fitToWindow = 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 currentTree property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree()
+ {
+ return currentTree;
+ }
- }
+ /**
+ * 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 columnWise property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isColumnWise()
+ {
+ if (columnWise == null)
+ {
+ return false;
+ }
+ else
+ {
+ return columnWise;
+ }
+ }
- /**
- * <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;
- }
+ /**
+ * 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 columnReference property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColumnReference()
+ {
+ return columnReference;
+ }
+
+ /**
+ * 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 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">
- * <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 linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews()
+ {
+ if (linkToAllViews == null)
+ {
+ return false;
+ }
+ else
+ {
+ return linkToAllViews;
+ }
+ }
- }
+ /**
+ * 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;
+ }
- /**
- * <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;
- }
+ /**
+ * 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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the xpos property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link Integer }
*
- * <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>
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
*
+ * @return possible object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "newick"
- })
- public static class Tree {
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- @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;
+ /**
+ * 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 title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ }
+
+ /**
+ * <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;
- /**
- * 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 userColourScheme property.
+ *
+ * @return possible object is {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme()
+ {
+ return userColourScheme;
+ }
- /**
- * Gets the value of the newick property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNewick() {
- return newick;
- }
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value)
+ {
+ this.userColourScheme = 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 id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * 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 fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = 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="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;
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBootstrap() {
- return showBootstrap;
- }
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
- /**
- * Sets the value of the showBootstrap property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
- }
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
- /**
- * Gets the value of the showDistances property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDistances() {
- return showDistances;
- }
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value) {
- this.showDistances = value;
- }
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked() {
- return markUnlinked;
- }
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value) {
- this.markUnlinked = value;
- }
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isFitToWindow() {
- return fitToWindow;
- }
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value) {
- this.fitToWindow = value;
- }
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
- /**
- * Gets the value of the currentTree property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCurrentTree() {
- return currentTree;
- }
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value) {
- this.currentTree = value;
- }
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
- /**
- * 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 = "charWidth")
+ protected Integer charWidth;
- /**
- * Sets the value of the columnWise property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColumnWise(Boolean value) {
- this.columnWise = value;
- }
+ @XmlAttribute(name = "charHeight")
+ protected Integer charHeight;
- /**
- * Gets the value of the columnReference property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColumnReference() {
- return columnReference;
- }
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
- /**
- * Sets the value of the columnReference property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColumnReference(String value) {
- this.columnReference = value;
- }
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
- /**
- * 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 = "viewName")
+ protected String viewName;
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
+
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ @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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * 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>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <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>
+ * getHiddenColumns().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ *
*/
- @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.
- *
- * @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;
- }
-
+ public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
+ {
+ if (hiddenColumns == null)
+ {
+ hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * 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>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <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>
+ * getCalcIdParam().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ *
*/
- @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 conservationSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value) {
- this.conservationSelected = value;
- }
-
- /**
- * Gets the value of the pidSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPidSelected() {
- return pidSelected;
- }
-
- /**
- * 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 bgColour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBgColour() {
- return bgColour;
- }
+ public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
+ {
+ if (calcIdParam == null)
+ {
+ calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
- /**
- * 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 overview property.
+ *
+ * @return possible object is {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview getOverview()
+ {
+ return overview;
+ }
- /**
- * Gets the value of the consThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ /**
+ * 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 consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected()
+ {
+ return conservationSelected;
+ }
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value)
+ {
+ this.conservationSelected = 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 pidSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected()
+ {
+ return pidSelected;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * 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 title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBgColour()
+ {
+ return bgColour;
+ }
- /**
- * Gets the value of the showFullId property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowFullId() {
- return showFullId;
- }
+ /**
+ * 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 showFullId property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value) {
- this.showFullId = value;
- }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRightAlignIds() {
- return rightAlignIds;
- }
+ /**
+ * 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 rightAlignIds property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value) {
- this.rightAlignIds = value;
- }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * Gets the value of the showText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowText() {
- return showText;
- }
+ /**
+ * 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 showText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowText(Boolean value) {
- this.showText = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Gets the value of the showColourText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowColourText() {
- return showColourText;
- }
+ /**
+ * 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 showColourText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value) {
- this.showColourText = value;
- }
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId()
+ {
+ return showFullId;
+ }
- /**
- * 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 showFullId property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value)
+ {
+ this.showFullId = 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 rightAlignIds property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
- /**
- * Gets the value of the showBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBoxes() {
- return showBoxes;
- }
+ /**
+ * 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 showBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value) {
- this.showBoxes = value;
- }
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowText()
+ {
+ return showText;
+ }
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isWrapAlignment() {
- return wrapAlignment;
- }
+ /**
+ * 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 wrapAlignment property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value) {
- this.wrapAlignment = value;
- }
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText()
+ {
+ return showColourText;
+ }
- /**
- * Gets the value of the renderGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRenderGaps() {
- return renderGaps;
- }
+ /**
+ * 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 renderGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value) {
- this.renderGaps = 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 showSequenceFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures() {
- return showSequenceFeatures;
- }
+ /**
+ * 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 showSequenceFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value) {
- this.showSequenceFeatures = value;
- }
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes()
+ {
+ return showBoxes;
+ }
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip() {
- return showNPfeatureTooltip;
- }
+ /**
+ * 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 showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value) {
- this.showNPfeatureTooltip = value;
- }
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment()
+ {
+ return wrapAlignment;
+ }
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip() {
- return showDbRefTooltip;
- }
+ /**
+ * 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 showDbRefTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value) {
- this.showDbRefTooltip = value;
- }
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps()
+ {
+ return renderGaps;
+ }
- /**
- * 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 renderGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value)
+ {
+ this.renderGaps = 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 showSequenceFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
- /**
- * 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 showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value)
+ {
+ this.showSequenceFeatures = 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 showNPfeatureTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip()
+ {
+ return showNPfeatureTooltip;
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowAnnotation() {
- return showAnnotation;
- }
+ /**
+ * 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 showAnnotation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value) {
- this.showAnnotation = value;
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip()
+ {
+ return showDbRefTooltip;
+ }
- /**
- * 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 showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value)
+ {
+ this.showDbRefTooltip = 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 followHighlight property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight()
+ {
+ if (followHighlight == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followHighlight;
+ }
+ }
- /**
- * 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 followHighlight property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value)
+ {
+ this.followHighlight = 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 followSelection property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection()
+ {
+ if (followSelection == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followSelection;
+ }
+ }
- /**
- * 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 followSelection property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value)
+ {
+ this.followSelection = 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 showAnnotation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
- /**
- * 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 showAnnotation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value)
+ {
+ this.showAnnotation = 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 centreColumnLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels()
+ {
+ if (centreColumnLabels == null)
+ {
+ return false;
+ }
+ else
+ {
+ return centreColumnLabels;
+ }
+ }
- /**
- * 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 centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value)
+ {
+ this.centreColumnLabels = 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 showGroupConservation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation()
+ {
+ if (showGroupConservation == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConservation;
+ }
+ }
- /**
- * 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 showGroupConservation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value)
+ {
+ this.showGroupConservation = 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 showGroupConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus()
+ {
+ if (showGroupConsensus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConsensus;
+ }
+ }
- /**
- * 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 showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value)
+ {
+ this.showGroupConsensus = 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 showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the startRes property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartRes() {
- return startRes;
- }
+ /**
+ * 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 startRes property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartRes(Integer value) {
- this.startRes = 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 startSeq property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartSeq() {
- return startSeq;
- }
+ /**
+ * 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 startSeq property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartSeq(Integer value) {
- this.startSeq = 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 charWidth property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getCharWidth() {
- return charWidth;
- }
+ /**
+ * 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 charWidth property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setCharWidth(Integer value) {
- this.charWidth = 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 charHeight property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getCharHeight() {
- return charHeight;
- }
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartRes()
+ {
+ return startRes;
+ }
- /**
- * 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 startRes property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value)
+ {
+ this.startRes = value;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartSeq()
+ {
+ return startSeq;
+ }
- /**
- * 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 startSeq property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value)
+ {
+ this.startSeq = value;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * Gets the value of the charWidth property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getCharWidth()
+ {
+ return charWidth;
+ }
- /**
- * 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 charWidth property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setCharWidth(Integer value)
+ {
+ this.charWidth = value;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * Gets the value of the charHeight property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getCharHeight()
+ {
+ return charHeight;
+ }
- /**
- * 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 charHeight property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setCharHeight(Integer value)
+ {
+ this.charHeight = 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 fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * 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 fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewName() {
- return viewName;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * 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 fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceSetId() {
- return sequenceSetId;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * 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 fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGatheredViews() {
- return gatheredViews;
- }
+ /**
+ * 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 gatheredViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value) {
- this.gatheredViews = 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 textCol1 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol1() {
- return textCol1;
- }
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewName()
+ {
+ return viewName;
+ }
- /**
- * 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 viewName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewName(String value)
+ {
+ this.viewName = value;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol2() {
- return textCol2;
- }
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceSetId()
+ {
+ return sequenceSetId;
+ }
- /**
- * 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 sequenceSetId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceSetId(String value)
+ {
+ this.sequenceSetId = value;
+ }
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextColThreshold() {
- return textColThreshold;
- }
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews()
+ {
+ return gatheredViews;
+ }
- /**
- * 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 gatheredViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value)
+ {
+ this.gatheredViews = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * 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 textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Gets the value of the complementId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComplementId() {
- return complementId;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * 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 textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = 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 textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * 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 textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = 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 id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * 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 id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Gets the value of the complementId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComplementId()
+ {
+ return complementId;
+ }
- /**
- * 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 complementId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComplementId(String value)
+ {
+ this.complementId = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * 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 height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = 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 xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * 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 xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = 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 ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * 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 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;
+ }
- /**
- * <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
- {
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- @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;
- }
+ /**
+ * 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;
+ }
- /**
- * <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;
- }
+ /**
+ * 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)
+ {
+ 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;
+ }
+ }
- /**
- * <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>
+ * <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>
+ * <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;
+ }
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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;
+@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
+ {
+
@XmlElement(namespace = "")
- protected List<JalviewUserColours.Filter> filter;
- @XmlAttribute(name = "schemeName")
- protected String schemeName;
+ 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 version property.
+ * 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 }
+ *
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getVersion() {
- return version;
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
}
/**
- * Sets the value of the version property.
+ * 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 }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setVersion(String value) {
- this.version = value;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Gets the value of the colour property.
+ * Gets the value of the rgb 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.
+ * @return possible object is {@link String }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getColour().add(newItem);
- * </pre>
+ */
+ public String getRGB()
+ {
+ return rgb;
+ }
+
+ /**
+ * Sets the value of the rgb property.
*
+ * @param value
+ * allowed object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Colour }
+ */
+ public void setRGB(String value)
+ {
+ this.rgb = value;
+ }
+
+ /**
+ * Gets the value of the minRGB property.
*
+ * @return possible object is {@link String }
*
*/
- public List<JalviewUserColours.Colour> getColour() {
- if (colour == null) {
- colour = new ArrayList<JalviewUserColours.Colour>();
- }
- return this.colour;
+ public String getMinRGB()
+ {
+ return minRGB;
}
/**
- * Gets the value of the filter property.
+ * Sets the value of the minRGB 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.
+ * @param value
+ * allowed object is {@link String }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getFilter().add(newItem);
- * </pre>
+ */
+ public void setMinRGB(String value)
+ {
+ this.minRGB = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
*
+ * @return possible object is {@link NoValueColour }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Filter }
+ */
+ 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 List<JalviewUserColours.Filter> getFilter() {
- if (filter == null) {
- filter = new ArrayList<JalviewUserColours.Filter>();
- }
- return this.filter;
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
}
/**
- * Gets the value of the schemeName property.
+ * Gets the value of the threshType property.
+ *
+ * @return possible object is {@link ThresholdType }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getSchemeName() {
- return schemeName;
+ public ThresholdType getThreshType()
+ {
+ return threshType;
}
/**
- * Sets the value of the schemeName property.
+ * Sets the value of the threshType property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link ThresholdType }
+ *
*/
- public void setSchemeName(String value) {
- this.schemeName = value;
+ 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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the threshold property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link Float }
*
- * <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>
+ */
+ 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 }
*
*/
- @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;
- }
+ 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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the colourByLabel property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <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>
+ */
+ 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="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.
+ *
+ * @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 }
*
*/
- @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;
- }
+ 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;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * Java class for mapListType complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="mapListType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = {
- "mapListFrom",
- "mapListTo"
-})
-@XmlSeeAlso({
- Mapping.class
-})
-public class MapListType {
+@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;
+ }
- 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 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;
/**
- * 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 }
- *
+ * Gets the value of the start property.
*
*/
- public List<MapListType.MapListFrom> getMapListFrom() {
- if (mapListFrom == null) {
- mapListFrom = new ArrayList<MapListType.MapListFrom>();
- }
- return this.mapListFrom;
+ public int getStart()
+ {
+ return start;
}
/**
- * 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 }
- *
+ * Sets the value of the start property.
*
*/
- public List<MapListType.MapListTo> getMapListTo() {
- if (mapListTo == null) {
- mapListTo = new ArrayList<MapListType.MapListTo>();
- }
- return this.mapListTo;
+ public void setStart(int value)
+ {
+ this.start = value;
}
/**
- * Gets the value of the mapFromUnit property.
+ * Gets the value of the end property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getMapFromUnit() {
- return mapFromUnit;
+ public int getEnd()
+ {
+ return end;
}
/**
- * Sets the value of the mapFromUnit property.
+ * Sets the value of the end property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
*/
- public void setMapFromUnit(BigInteger value) {
- this.mapFromUnit = value;
+ public void setEnd(int 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">
+ * <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 mapToUnit property.
+ * Gets the value of the start property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getMapToUnit() {
- return mapToUnit;
+ public int getStart()
+ {
+ return start;
}
/**
- * Sets the value of the mapToUnit property.
+ * Sets the value of the start property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
*/
- public void setMapToUnit(BigInteger value) {
- this.mapToUnit = value;
+ public void setStart(int value)
+ {
+ this.start = 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>
- *
+ * Gets the value of the end property.
*
*/
- @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;
- }
-
+ public int getEnd()
+ {
+ return end;
}
-
/**
- * <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>
- *
+ * Sets the value of the end property.
*
*/
- @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;
- }
-
+ public void setEnd(int value)
+ {
+ this.end = value;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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>
*
*/
@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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 PM BST
//
-
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for MatrixType complex type.
+ * <p>
+ * Java class for MatrixType 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="MatrixType">
*
*/
@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;
- }
+@XmlType(
+ name = "MatrixType",
+ propOrder =
+ { "elements", "groups", "newick", "property", "mapping" })
+public class MatrixType
+{
- /**
- * Sets the value of the elements property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setElements(String value) {
- this.elements = value;
- }
+ @XmlElement(required = true)
+ protected String elements;
- /**
- * 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;
- }
+ protected List<String> 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>();
- }
- return this.newick;
- }
+ protected List<String> 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>();
- }
- return this.property;
- }
+ protected List<Property> property;
- /**
- * Gets the value of the mapping property.
- *
- * @return
- * possible object is
- * {@link MapListType }
- *
- */
- public MapListType getMapping() {
- return mapping;
- }
+ protected MapListType mapping;
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link MapListType }
- *
- */
- public void setMapping(MapListType value) {
- this.mapping = value;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "rows", required = true)
+ protected BigInteger rows;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ @XmlAttribute(name = "cols", required = true)
+ protected BigInteger cols;
- /**
- * Gets the value of the rows property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getRows() {
- return rows;
- }
+ @XmlAttribute(name = "treeMethod")
+ protected String treeMethod;
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setRows(BigInteger value) {
- this.rows = value;
- }
+ @XmlAttribute(name = "cutHeight")
+ protected Double cutHeight;
- /**
- * Gets the value of the cols property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getCols() {
- return cols;
- }
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * 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 elements property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getElements()
+ {
+ return elements;
+ }
- /**
- * Gets the value of the treeMethod property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTreeMethod() {
- return treeMethod;
- }
+ /**
+ * Sets the value of the elements property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setElements(String value)
+ {
+ this.elements = 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 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;
+ }
- /**
- * Gets the value of the cutHeight property.
- *
- * @return
- * possible object is
- * {@link Double }
- *
- */
- public Double getCutHeight() {
- return cutHeight;
+ /**
+ * 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 cutHeight property.
- *
- * @param value
- * allowed object is
- * {@link Double }
- *
- */
- public void setCutHeight(Double value) {
- this.cutHeight = 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 id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the mapping property.
+ *
+ * @return possible object is {@link MapListType }
+ *
+ */
+ public MapListType getMapping()
+ {
+ return mapping;
+ }
- /**
- * 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 mapping property.
+ *
+ * @param value
+ * allowed object is {@link MapListType }
+ *
+ */
+ public void setMapping(MapListType value)
+ {
+ this.mapping = 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 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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>
+ * 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">
*/
@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
+{
- public String value() {
- return value;
- }
+ @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 static NoValueColour fromValue(String v) {
- for (NoValueColour c: NoValueColour.values()) {
- if (c.value.equals(v)) {
- return c;
- }
- }
- throw new IllegalArgumentException(v);
+ public static NoValueColour fromValue(String v)
+ {
+ for (NoValueColour c : NoValueColour.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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 _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);
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
- "pairwiseMatrix",
- "tridiagonalMatrix",
- "eigenMatrix"
-})
-public class PcaDataType {
+@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;
- @XmlElement(required = true)
- protected DoubleMatrix pairwiseMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix tridiagonalMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix eigenMatrix;
+ @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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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;
+@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;
/**
- * Gets the value of the id property.
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public String getName()
+ {
+ return name;
}
/**
- * Sets the value of the id property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the type property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Sets the value of the type property.
+ * Gets the value of the value 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 }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getFile() {
- return file;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the file property.
+ * Sets the value of the value 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>
- *
+ * allowed object is {@link String }
*
*/
- @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;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "property")
-public class Property {
+public class Property
+{
+
+ @XmlAttribute(name = "name")
+ protected String name;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "value")
- protected String value;
+ @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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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>
*
*/
@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;
+ @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;
/**
- * Gets the value of the dbRef property.
+ * Gets the value of the mapping 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.
+ * @return possible object is {@link Mapping }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDBRef().add(newItem);
- * </pre>
+ */
+ 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 }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Sequence.DBRef }
+ */
+ public String getSource()
+ {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<Sequence.DBRef> getDBRef() {
- if (dbRef == null) {
- dbRef = new ArrayList<Sequence.DBRef>();
- }
- return this.dbRef;
+ public void setSource(String value)
+ {
+ this.source = value;
}
/**
- * Gets the value of the dsseqid property.
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDsseqid() {
- return dsseqid;
+ public String getVersion()
+ {
+ return version;
}
/**
- * Sets the value of the dsseqid property.
+ * Sets the value of the version property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setDsseqid(String value) {
- this.dsseqid = value;
+ public void setVersion(String value)
+ {
+ this.version = value;
}
/**
- * Gets the value of the biotype property.
+ * Gets the value of the accessionId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getBiotype() {
- return biotype;
+ public String getAccessionId()
+ {
+ return accessionId;
}
/**
- * Sets the value of the biotype property.
+ * Sets the value of the accessionId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setBiotype(String value) {
- this.biotype = value;
+ 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;
+ }
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the locus property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <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>
+ */
+ public void setLocus(Boolean value)
+ {
+ this.locus = value;
+ }
+
+ /**
+ * Gets the value of the canonical property.
*
+ * @return possible object is {@link Boolean }
*
*/
- @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;
- }
+ 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;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "sequence",
- "annotation",
- "sequenceSetProperties",
- "alcodonFrame"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
@XmlRootElement(name = "SequenceSet")
-public class SequenceSet {
+public class SequenceSet
+{
- @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;
- @XmlAttribute(name = "gapChar", required = true)
- protected String gapChar;
- @XmlAttribute(name = "datasetId")
- protected String datasetId;
+ @XmlElement(name = "Sequence")
+ protected List<Sequence> 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;
+ @XmlElement(name = "Annotation")
+ protected List<Annotation> annotation;
+
+ protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+
+ @XmlElement(name = "AlcodonFrame")
+ protected List<AlcodonFrame> alcodonFrame;
+
+ @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>();
}
+ 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>();
- }
- return this.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;
+ }
- /**
- * 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;
+ /**
+ * 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;
+ }
- /**
- * 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;
+ /**
+ * 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;
+ }
+
+ /**
+ * 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 gapChar property.
+ * Gets the value of the key property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getGapChar() {
- return gapChar;
+ public String getKey()
+ {
+ return key;
}
/**
- * Sets the value of the gapChar property.
+ * Sets the value of the key property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGapChar(String value) {
- this.gapChar = value;
- }
-
- /**
- * Gets the value of the datasetId property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDatasetId() {
- return datasetId;
+ public void setKey(String value)
+ {
+ this.key = value;
}
/**
- * Sets the value of the datasetId property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setDatasetId(String value) {
- this.datasetId = value;
+ public String getValue()
+ {
+ return 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>
+ * Sets the value of the value property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @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;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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>
+ * Java class for ThresholdType.
*
- * <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.
+ * <p>
+ *
* <pre>
* <simpleType name="ThresholdType">
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
*/
@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);
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = {
- "tree",
- "sequenceSet"
-})
-public class VAMSAS {
+@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
+public class VAMSAS
+{
+
+ @XmlElement(name = "Tree")
+ protected List<String> tree;
- @XmlElement(name = "Tree")
- protected List<String> tree;
- @XmlElement(name = "SequenceSet")
- protected List<SequenceSet> sequenceSet;
+ @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>();
- }
- return this.tree;
+ /**
+ * 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;
+ }
- /**
- * 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;
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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">
*
*/
@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>();
- }
- 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;
+ 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:41 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;
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes different types of citations.
- * Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
+ * Describes different types of citations. Equivalent to the flat file RX-, RG-,
+ * RA-, RT- and RL-lines.
*
- * <p>Java class for citationType complex type.
+ * <p>
+ * Java class for citationType 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="citationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "citationType", propOrder = {
- "title",
- "editorList",
- "authorList",
- "locator",
- "dbReference"
-})
-public class CitationType {
-
- protected String title;
- protected NameListType editorList;
- protected NameListType authorList;
- protected String locator;
- protected List<DbReferenceType> dbReference;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "date")
- protected String date;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "volume")
- protected String volume;
- @XmlAttribute(name = "first")
- protected String first;
- @XmlAttribute(name = "last")
- protected String last;
- @XmlAttribute(name = "publisher")
- protected String publisher;
- @XmlAttribute(name = "city")
- protected String city;
- @XmlAttribute(name = "db")
- protected String db;
- @XmlAttribute(name = "number")
- protected String number;
- @XmlAttribute(name = "institute")
- protected String institute;
- @XmlAttribute(name = "country")
- protected String country;
-
- /**
- * 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 editorList property.
- *
- * @return
- * possible object is
- * {@link NameListType }
- *
- */
- public NameListType getEditorList() {
- return editorList;
- }
-
- /**
- * Sets the value of the editorList property.
- *
- * @param value
- * allowed object is
- * {@link NameListType }
- *
- */
- public void setEditorList(NameListType value) {
- this.editorList = value;
- }
-
- /**
- * Gets the value of the authorList property.
- *
- * @return
- * possible object is
- * {@link NameListType }
- *
- */
- public NameListType getAuthorList() {
- return authorList;
- }
-
- /**
- * Sets the value of the authorList property.
- *
- * @param value
- * allowed object is
- * {@link NameListType }
- *
- */
- public void setAuthorList(NameListType value) {
- this.authorList = value;
- }
-
- /**
- * Gets the value of the locator property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLocator() {
- return locator;
- }
-
- /**
- * Sets the value of the locator property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocator(String value) {
- this.locator = value;
- }
-
- /**
- * Gets the value of the dbReference 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 dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
- }
-
- /**
- * 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 date property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDate() {
- return date;
- }
-
- /**
- * Sets the value of the date property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDate(String value) {
- this.date = 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 volume property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVolume() {
- return volume;
- }
-
- /**
- * Sets the value of the volume property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVolume(String value) {
- this.volume = value;
- }
-
- /**
- * Gets the value of the first property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFirst() {
- return first;
- }
-
- /**
- * Sets the value of the first property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFirst(String value) {
- this.first = value;
- }
-
- /**
- * Gets the value of the last property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLast() {
- return last;
- }
-
- /**
- * Sets the value of the last property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLast(String value) {
- this.last = value;
- }
-
- /**
- * Gets the value of the publisher property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getPublisher() {
- return publisher;
- }
-
- /**
- * Sets the value of the publisher property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setPublisher(String value) {
- this.publisher = value;
- }
-
- /**
- * Gets the value of the city property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCity() {
- return city;
- }
-
- /**
- * Sets the value of the city property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCity(String value) {
- this.city = value;
- }
-
- /**
- * Gets the value of the db property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDb() {
- return db;
- }
-
- /**
- * Sets the value of the db property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDb(String value) {
- this.db = value;
- }
-
- /**
- * Gets the value of the number property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNumber() {
- return number;
- }
-
- /**
- * Sets the value of the number property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNumber(String value) {
- this.number = value;
- }
-
- /**
- * Gets the value of the institute property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getInstitute() {
- return institute;
- }
-
- /**
- * Sets the value of the institute property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setInstitute(String value) {
- this.institute = value;
- }
-
- /**
- * Gets the value of the country property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCountry() {
- return country;
- }
-
- /**
- * Sets the value of the country property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCountry(String value) {
- this.country = value;
- }
+@XmlType(
+ name = "citationType",
+ propOrder =
+ { "title", "editorList", "authorList", "locator", "dbReference" })
+public class CitationType
+{
+
+ protected String title;
+
+ protected NameListType editorList;
+
+ protected NameListType authorList;
+
+ protected String locator;
+
+ protected List<DbReferenceType> dbReference;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "date")
+ protected String date;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "volume")
+ protected String volume;
+
+ @XmlAttribute(name = "first")
+ protected String first;
+
+ @XmlAttribute(name = "last")
+ protected String last;
+
+ @XmlAttribute(name = "publisher")
+ protected String publisher;
+
+ @XmlAttribute(name = "city")
+ protected String city;
+
+ @XmlAttribute(name = "db")
+ protected String db;
+
+ @XmlAttribute(name = "number")
+ protected String number;
+
+ @XmlAttribute(name = "institute")
+ protected String institute;
+
+ @XmlAttribute(name = "country")
+ protected String country;
+
+ /**
+ * 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 editorList property.
+ *
+ * @return possible object is {@link NameListType }
+ *
+ */
+ public NameListType getEditorList()
+ {
+ return editorList;
+ }
+
+ /**
+ * Sets the value of the editorList property.
+ *
+ * @param value
+ * allowed object is {@link NameListType }
+ *
+ */
+ public void setEditorList(NameListType value)
+ {
+ this.editorList = value;
+ }
+
+ /**
+ * Gets the value of the authorList property.
+ *
+ * @return possible object is {@link NameListType }
+ *
+ */
+ public NameListType getAuthorList()
+ {
+ return authorList;
+ }
+
+ /**
+ * Sets the value of the authorList property.
+ *
+ * @param value
+ * allowed object is {@link NameListType }
+ *
+ */
+ public void setAuthorList(NameListType value)
+ {
+ this.authorList = value;
+ }
+
+ /**
+ * Gets the value of the locator property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLocator()
+ {
+ return locator;
+ }
+
+ /**
+ * Sets the value of the locator property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLocator(String value)
+ {
+ this.locator = value;
+ }
+
+ /**
+ * Gets the value of the dbReference 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 dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * 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 date property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDate()
+ {
+ return date;
+ }
+
+ /**
+ * Sets the value of the date property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDate(String value)
+ {
+ this.date = 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 volume property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVolume()
+ {
+ return volume;
+ }
+
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVolume(String value)
+ {
+ this.volume = value;
+ }
+
+ /**
+ * Gets the value of the first property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFirst()
+ {
+ return first;
+ }
+
+ /**
+ * Sets the value of the first property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFirst(String value)
+ {
+ this.first = value;
+ }
+
+ /**
+ * Gets the value of the last property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLast()
+ {
+ return last;
+ }
+
+ /**
+ * Sets the value of the last property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLast(String value)
+ {
+ this.last = value;
+ }
+
+ /**
+ * Gets the value of the publisher property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getPublisher()
+ {
+ return publisher;
+ }
+
+ /**
+ * Sets the value of the publisher property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setPublisher(String value)
+ {
+ this.publisher = value;
+ }
+
+ /**
+ * Gets the value of the city property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCity()
+ {
+ return city;
+ }
+
+ /**
+ * Sets the value of the city property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCity(String value)
+ {
+ this.city = value;
+ }
+
+ /**
+ * Gets the value of the db property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDb()
+ {
+ return db;
+ }
+
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDb(String value)
+ {
+ this.db = value;
+ }
+
+ /**
+ * Gets the value of the number property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNumber()
+ {
+ return number;
+ }
+
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNumber(String value)
+ {
+ this.number = value;
+ }
+
+ /**
+ * Gets the value of the institute property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getInstitute()
+ {
+ return institute;
+ }
+
+ /**
+ * Sets the value of the institute property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setInstitute(String value)
+ {
+ this.institute = value;
+ }
+
+ /**
+ * Gets the value of the country property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCountry()
+ {
+ return country;
+ }
+
+ /**
+ * Sets the value of the country property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCountry(String value)
+ {
+ this.country = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes a cofactor.
*
- * <p>Java class for cofactorType complex type.
+ * <p>
+ * Java class for cofactorType 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="cofactorType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cofactorType", propOrder = {
- "name",
- "dbReference"
-})
-public class CofactorType {
+@XmlType(name = "cofactorType", propOrder = { "name", "dbReference" })
+public class CofactorType
+{
- @XmlElement(required = true)
- protected String name;
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected String name;
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = 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 dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
+
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes different types of general annotations.
- * Equivalent to the flat file CC-line.
+ * Describes different types of general annotations. Equivalent to the flat file
+ * CC-line.
*
- * <p>Java class for commentType complex type.
+ * <p>
+ * Java class for commentType 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="commentType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "commentType", propOrder = {
- "molecule",
- "absorption",
- "kinetics",
- "phDependence",
- "redoxPotential",
- "temperatureDependence",
- "reaction",
- "physiologicalReaction",
- "cofactor",
- "subcellularLocation",
- "conflict",
- "link",
- "event",
- "isoform",
- "interactant",
- "organismsDiffer",
- "experiments",
- "disease",
- "location",
- "text"
-})
-public class CommentType {
-
- protected MoleculeType molecule;
- protected CommentType.Absorption absorption;
- protected CommentType.Kinetics kinetics;
- protected CommentType.PhDependence phDependence;
- protected CommentType.RedoxPotential redoxPotential;
- protected CommentType.TemperatureDependence temperatureDependence;
- protected ReactionType reaction;
- protected List<PhysiologicalReactionType> physiologicalReaction;
- protected List<CofactorType> cofactor;
- protected List<SubcellularLocationType> subcellularLocation;
- protected CommentType.Conflict conflict;
- protected List<CommentType.Link> link;
- protected List<EventType> event;
- protected List<IsoformType> isoform;
- protected List<InteractantType> interactant;
- @XmlElement(defaultValue = "false")
- protected Boolean organismsDiffer;
- protected Integer experiments;
- protected CommentType.Disease disease;
- protected List<LocationType> location;
- protected List<EvidencedStringType> text;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "locationType")
- protected String locationType;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "mass")
- protected Float mass;
- @XmlAttribute(name = "error")
- protected String error;
- @XmlAttribute(name = "method")
- protected String method;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+@XmlType(
+ name = "commentType",
+ propOrder =
+ { "molecule", "absorption", "kinetics", "phDependence", "redoxPotential",
+ "temperatureDependence", "reaction", "physiologicalReaction",
+ "cofactor", "subcellularLocation", "conflict", "link", "event",
+ "isoform", "interactant", "organismsDiffer", "experiments", "disease",
+ "location", "text" })
+public class CommentType
+{
- /**
- * Gets the value of the molecule property.
- *
- * @return
- * possible object is
- * {@link MoleculeType }
- *
- */
- public MoleculeType getMolecule() {
- return molecule;
- }
+ protected MoleculeType molecule;
- /**
- * Sets the value of the molecule property.
- *
- * @param value
- * allowed object is
- * {@link MoleculeType }
- *
- */
- public void setMolecule(MoleculeType value) {
- this.molecule = value;
- }
+ protected CommentType.Absorption absorption;
- /**
- * Gets the value of the absorption property.
- *
- * @return
- * possible object is
- * {@link CommentType.Absorption }
- *
- */
- public CommentType.Absorption getAbsorption() {
- return absorption;
- }
+ protected CommentType.Kinetics kinetics;
- /**
- * Sets the value of the absorption property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Absorption }
- *
- */
- public void setAbsorption(CommentType.Absorption value) {
- this.absorption = value;
- }
+ protected CommentType.PhDependence phDependence;
- /**
- * Gets the value of the kinetics property.
- *
- * @return
- * possible object is
- * {@link CommentType.Kinetics }
- *
- */
- public CommentType.Kinetics getKinetics() {
- return kinetics;
- }
+ protected CommentType.RedoxPotential redoxPotential;
- /**
- * Sets the value of the kinetics property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Kinetics }
- *
- */
- public void setKinetics(CommentType.Kinetics value) {
- this.kinetics = value;
- }
+ protected CommentType.TemperatureDependence temperatureDependence;
- /**
- * Gets the value of the phDependence property.
- *
- * @return
- * possible object is
- * {@link CommentType.PhDependence }
- *
- */
- public CommentType.PhDependence getPhDependence() {
- return phDependence;
- }
+ protected ReactionType reaction;
- /**
- * Sets the value of the phDependence property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.PhDependence }
- *
- */
- public void setPhDependence(CommentType.PhDependence value) {
- this.phDependence = value;
- }
+ protected List<PhysiologicalReactionType> physiologicalReaction;
- /**
- * Gets the value of the redoxPotential property.
- *
- * @return
- * possible object is
- * {@link CommentType.RedoxPotential }
- *
- */
- public CommentType.RedoxPotential getRedoxPotential() {
- return redoxPotential;
- }
+ protected List<CofactorType> cofactor;
- /**
- * Sets the value of the redoxPotential property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.RedoxPotential }
- *
- */
- public void setRedoxPotential(CommentType.RedoxPotential value) {
- this.redoxPotential = value;
- }
+ protected List<SubcellularLocationType> subcellularLocation;
- /**
- * Gets the value of the temperatureDependence property.
- *
- * @return
- * possible object is
- * {@link CommentType.TemperatureDependence }
- *
- */
- public CommentType.TemperatureDependence getTemperatureDependence() {
- return temperatureDependence;
- }
+ protected CommentType.Conflict conflict;
- /**
- * Sets the value of the temperatureDependence property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.TemperatureDependence }
- *
- */
- public void setTemperatureDependence(CommentType.TemperatureDependence value) {
- this.temperatureDependence = value;
+ protected List<CommentType.Link> link;
+
+ protected List<EventType> event;
+
+ protected List<IsoformType> isoform;
+
+ protected List<InteractantType> interactant;
+
+ @XmlElement(defaultValue = "false")
+ protected Boolean organismsDiffer;
+
+ protected Integer experiments;
+
+ protected CommentType.Disease disease;
+
+ protected List<LocationType> location;
+
+ protected List<EvidencedStringType> text;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "locationType")
+ protected String locationType;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "mass")
+ protected Float mass;
+
+ @XmlAttribute(name = "error")
+ protected String error;
+
+ @XmlAttribute(name = "method")
+ protected String method;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return possible object is {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule()
+ {
+ return molecule;
+ }
+
+ /**
+ * Sets the value of the molecule property.
+ *
+ * @param value
+ * allowed object is {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value)
+ {
+ this.molecule = value;
+ }
+
+ /**
+ * Gets the value of the absorption property.
+ *
+ * @return possible object is {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption getAbsorption()
+ {
+ return absorption;
+ }
+
+ /**
+ * Sets the value of the absorption property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Absorption }
+ *
+ */
+ public void setAbsorption(CommentType.Absorption value)
+ {
+ this.absorption = value;
+ }
+
+ /**
+ * Gets the value of the kinetics property.
+ *
+ * @return possible object is {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics getKinetics()
+ {
+ return kinetics;
+ }
+
+ /**
+ * Sets the value of the kinetics property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Kinetics }
+ *
+ */
+ public void setKinetics(CommentType.Kinetics value)
+ {
+ this.kinetics = value;
+ }
+
+ /**
+ * Gets the value of the phDependence property.
+ *
+ * @return possible object is {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence getPhDependence()
+ {
+ return phDependence;
+ }
+
+ /**
+ * Sets the value of the phDependence property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.PhDependence }
+ *
+ */
+ public void setPhDependence(CommentType.PhDependence value)
+ {
+ this.phDependence = value;
+ }
+
+ /**
+ * Gets the value of the redoxPotential property.
+ *
+ * @return possible object is {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential getRedoxPotential()
+ {
+ return redoxPotential;
+ }
+
+ /**
+ * Sets the value of the redoxPotential property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.RedoxPotential }
+ *
+ */
+ public void setRedoxPotential(CommentType.RedoxPotential value)
+ {
+ this.redoxPotential = value;
+ }
+
+ /**
+ * Gets the value of the temperatureDependence property.
+ *
+ * @return possible object is {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence getTemperatureDependence()
+ {
+ return temperatureDependence;
+ }
+
+ /**
+ * Sets the value of the temperatureDependence property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.TemperatureDependence }
+ *
+ */
+ public void setTemperatureDependence(
+ CommentType.TemperatureDependence value)
+ {
+ this.temperatureDependence = value;
+ }
+
+ /**
+ * Gets the value of the reaction property.
+ *
+ * @return possible object is {@link ReactionType }
+ *
+ */
+ public ReactionType getReaction()
+ {
+ return reaction;
+ }
+
+ /**
+ * Sets the value of the reaction property.
+ *
+ * @param value
+ * allowed object is {@link ReactionType }
+ *
+ */
+ public void setReaction(ReactionType value)
+ {
+ this.reaction = value;
+ }
+
+ /**
+ * Gets the value of the physiologicalReaction 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 physiologicalReaction property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getPhysiologicalReaction().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link PhysiologicalReactionType }
+ *
+ *
+ */
+ public List<PhysiologicalReactionType> getPhysiologicalReaction()
+ {
+ if (physiologicalReaction == null)
+ {
+ physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
+ }
+ return this.physiologicalReaction;
+ }
+
+ /**
+ * Gets the value of the cofactor 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 cofactor property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCofactor().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CofactorType }
+ *
+ *
+ */
+ public List<CofactorType> getCofactor()
+ {
+ if (cofactor == null)
+ {
+ cofactor = new ArrayList<CofactorType>();
+ }
+ return this.cofactor;
+ }
+
+ /**
+ * Gets the value of the subcellularLocation 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 subcellularLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSubcellularLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SubcellularLocationType }
+ *
+ *
+ */
+ public List<SubcellularLocationType> getSubcellularLocation()
+ {
+ if (subcellularLocation == null)
+ {
+ subcellularLocation = new ArrayList<SubcellularLocationType>();
+ }
+ return this.subcellularLocation;
+ }
+
+ /**
+ * Gets the value of the conflict property.
+ *
+ * @return possible object is {@link CommentType.Conflict }
+ *
+ */
+ public CommentType.Conflict getConflict()
+ {
+ return conflict;
+ }
+
+ /**
+ * Sets the value of the conflict property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Conflict }
+ *
+ */
+ public void setConflict(CommentType.Conflict value)
+ {
+ this.conflict = value;
+ }
+
+ /**
+ * Gets the value of the link 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 link property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getLink().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CommentType.Link }
+ *
+ *
+ */
+ public List<CommentType.Link> getLink()
+ {
+ if (link == null)
+ {
+ link = new ArrayList<CommentType.Link>();
}
+ return this.link;
+ }
+
+ /**
+ * Gets the value of the event 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 event property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvent().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link EventType }
+ *
+ *
+ */
+ public List<EventType> getEvent()
+ {
+ if (event == null)
+ {
+ event = new ArrayList<EventType>();
+ }
+ return this.event;
+ }
+
+ /**
+ * Gets the value of the isoform 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 isoform property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getIsoform().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link IsoformType
+ * }
+ *
+ *
+ */
+ public List<IsoformType> getIsoform()
+ {
+ if (isoform == null)
+ {
+ isoform = new ArrayList<IsoformType>();
+ }
+ return this.isoform;
+ }
+
+ /**
+ * Gets the value of the interactant 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 interactant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getInteractant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link InteractantType }
+ *
+ *
+ */
+ public List<InteractantType> getInteractant()
+ {
+ if (interactant == null)
+ {
+ interactant = new ArrayList<InteractantType>();
+ }
+ return this.interactant;
+ }
+
+ /**
+ * Gets the value of the organismsDiffer property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isOrganismsDiffer()
+ {
+ return organismsDiffer;
+ }
+
+ /**
+ * Sets the value of the organismsDiffer property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setOrganismsDiffer(Boolean value)
+ {
+ this.organismsDiffer = value;
+ }
+
+ /**
+ * Gets the value of the experiments property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getExperiments()
+ {
+ return experiments;
+ }
+
+ /**
+ * Sets the value of the experiments property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setExperiments(Integer value)
+ {
+ this.experiments = value;
+ }
+
+ /**
+ * Gets the value of the disease property.
+ *
+ * @return possible object is {@link CommentType.Disease }
+ *
+ */
+ public CommentType.Disease getDisease()
+ {
+ return disease;
+ }
+
+ /**
+ * Sets the value of the disease property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Disease }
+ *
+ */
+ public void setDisease(CommentType.Disease value)
+ {
+ this.disease = value;
+ }
+
+ /**
+ * Gets the value of the location 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 location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link LocationType }
+ *
+ *
+ */
+ public List<LocationType> getLocation()
+ {
+ if (location == null)
+ {
+ location = new ArrayList<LocationType>();
+ }
+ return this.location;
+ }
+
+ /**
+ * Gets the value of the text 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 text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ /**
+ * 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 locationType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLocationType()
+ {
+ return locationType;
+ }
+
+ /**
+ * Sets the value of the locationType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLocationType(String value)
+ {
+ this.locationType = 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 mass property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMass()
+ {
+ return mass;
+ }
+
+ /**
+ * Sets the value of the mass property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMass(Float value)
+ {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the error property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getError()
+ {
+ return error;
+ }
+
+ /**
+ * Sets the value of the error property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setError(String value)
+ {
+ this.error = value;
+ }
+
+ /**
+ * Gets the value of the method property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMethod()
+ {
+ return method;
+ }
+
+ /**
+ * Sets the value of the method property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMethod(String value)
+ {
+ this.method = value;
+ }
+
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * <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="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "max", "text" })
+ public static class Absorption
+ {
+
+ protected EvidencedStringType max;
+
+ protected List<EvidencedStringType> text;
/**
- * Gets the value of the reaction property.
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link EvidencedStringType }
*
- * @return
- * possible object is
- * {@link ReactionType }
- *
*/
- public ReactionType getReaction() {
- return reaction;
+ public EvidencedStringType getMax()
+ {
+ return max;
}
/**
- * Sets the value of the reaction property.
+ * Sets the value of the max property.
*
* @param value
- * allowed object is
- * {@link ReactionType }
- *
+ * allowed object is {@link EvidencedStringType }
+ *
*/
- public void setReaction(ReactionType value) {
- this.reaction = value;
+ public void setMax(EvidencedStringType value)
+ {
+ this.max = value;
}
/**
- * Gets the value of the physiologicalReaction property.
+ * Gets the value of the text 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 physiologicalReaction property.
+ * 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 text property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getPhysiologicalReaction().add(newItem);
+ * getText().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link PhysiologicalReactionType }
+ * {@link EvidencedStringType }
*
*
*/
- public List<PhysiologicalReactionType> getPhysiologicalReaction() {
- if (physiologicalReaction == null) {
- physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
- }
- return this.physiologicalReaction;
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <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="sequence" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="frameshift"/>
+ * <enumeration value="erroneous initiation"/>
+ * <enumeration value="erroneous termination"/>
+ * <enumeration value="erroneous gene model prediction"/>
+ * <enumeration value="erroneous translation"/>
+ * <enumeration value="miscellaneous discrepancy"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "sequence" })
+ public static class Conflict
+ {
+
+ protected CommentType.Conflict.Sequence sequence;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "ref")
+ protected String ref;
+
/**
- * Gets the value of the cofactor 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 cofactor property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCofactor().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CofactorType }
+ * Gets the value of the sequence property.
*
+ * @return possible object is {@link CommentType.Conflict.Sequence }
*
*/
- public List<CofactorType> getCofactor() {
- if (cofactor == null) {
- cofactor = new ArrayList<CofactorType>();
- }
- return this.cofactor;
+ public CommentType.Conflict.Sequence getSequence()
+ {
+ return sequence;
}
/**
- * Gets the value of the subcellularLocation 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 subcellularLocation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSubcellularLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SubcellularLocationType }
+ * Sets the value of the sequence property.
*
+ * @param value
+ * allowed object is {@link CommentType.Conflict.Sequence }
*
*/
- public List<SubcellularLocationType> getSubcellularLocation() {
- if (subcellularLocation == null) {
- subcellularLocation = new ArrayList<SubcellularLocationType>();
- }
- return this.subcellularLocation;
+ public void setSequence(CommentType.Conflict.Sequence value)
+ {
+ this.sequence = value;
}
/**
- * Gets the value of the conflict property.
+ * Gets the value of the type property.
*
- * @return
- * possible object is
- * {@link CommentType.Conflict }
- *
- */
- public CommentType.Conflict getConflict() {
- return conflict;
- }
-
- /**
- * Sets the value of the conflict property.
+ * @return possible object is {@link String }
*
- * @param value
- * allowed object is
- * {@link CommentType.Conflict }
- *
*/
- public void setConflict(CommentType.Conflict value) {
- this.conflict = value;
+ public String getType()
+ {
+ return type;
}
/**
- * Gets the value of the link 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 link property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getLink().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CommentType.Link }
+ * Sets the value of the type property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<CommentType.Link> getLink() {
- if (link == null) {
- link = new ArrayList<CommentType.Link>();
- }
- return this.link;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the event 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 event property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvent().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EventType }
+ * Gets the value of the ref property.
*
+ * @return possible object is {@link String }
*
*/
- public List<EventType> getEvent() {
- if (event == null) {
- event = new ArrayList<EventType>();
- }
- return this.event;
+ public String getRef()
+ {
+ return ref;
}
/**
- * Gets the value of the isoform 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 isoform property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getIsoform().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link IsoformType }
+ * Sets the value of the ref property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<IsoformType> getIsoform() {
- if (isoform == null) {
- isoform = new ArrayList<IsoformType>();
- }
- return this.isoform;
+ public void setRef(String value)
+ {
+ this.ref = value;
}
/**
- * Gets the value of the interactant 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 interactant property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getInteractant().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link InteractantType }
- *
- *
*/
- public List<InteractantType> getInteractant() {
- if (interactant == null) {
- interactant = new ArrayList<InteractantType>();
- }
- return this.interactant;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence
+ {
+
+ @XmlAttribute(name = "resource", required = true)
+ protected String resource;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ @XmlAttribute(name = "version")
+ protected Integer version;
+
+ /**
+ * Gets the value of the resource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getResource()
+ {
+ return resource;
+ }
+
+ /**
+ * Sets the value of the resource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setResource(String value)
+ {
+ this.resource = 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 version property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setVersion(Integer value)
+ {
+ this.version = value;
+ }
- /**
- * Gets the value of the organismsDiffer property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isOrganismsDiffer() {
- return organismsDiffer;
}
- /**
- * Sets the value of the organismsDiffer property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setOrganismsDiffer(Boolean value) {
- this.organismsDiffer = 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="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ * </sequence>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "name", "acronym", "description", "dbReference" })
+ public static class Disease
+ {
+
+ @XmlElement(required = true)
+ protected String name;
- /**
- * Gets the value of the experiments property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getExperiments() {
- return experiments;
- }
+ @XmlElement(required = true)
+ protected String acronym;
- /**
- * Sets the value of the experiments property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setExperiments(Integer value) {
- this.experiments = value;
- }
+ @XmlElement(required = true)
+ protected String description;
- /**
- * Gets the value of the disease property.
- *
- * @return
- * possible object is
- * {@link CommentType.Disease }
- *
- */
- public CommentType.Disease getDisease() {
- return disease;
- }
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Sets the value of the disease property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Disease }
- *
- */
- public void setDisease(CommentType.Disease value) {
- this.disease = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
/**
- * Gets the value of the location 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 location property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link LocationType }
+ * Gets the value of the name property.
*
+ * @return possible object is {@link String }
*
*/
- public List<LocationType> getLocation() {
- if (location == null) {
- location = new ArrayList<LocationType>();
- }
- return this.location;
+ public String getName()
+ {
+ return name;
}
/**
- * Gets the value of the text 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 text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
+ * Sets the value of the name property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Gets the value of the type property.
+ * Gets the value of the acronym property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public String getAcronym()
+ {
+ return acronym;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the acronym property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the locationType property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getLocationType() {
- return locationType;
+ public void setAcronym(String value)
+ {
+ this.acronym = value;
}
/**
- * Sets the value of the locationType property.
+ * Gets the value of the description property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocationType(String value) {
- this.locationType = value;
- }
-
- /**
- * Gets the value of the name property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getName() {
- return name;
+ public String getDescription()
+ {
+ return description;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the description property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the mass property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Float }
- *
*/
- public Float getMass() {
- return mass;
+ public void setDescription(String value)
+ {
+ this.description = value;
}
/**
- * Sets the value of the mass property.
+ * Gets the value of the dbReference property.
*
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMass(Float value) {
- this.mass = value;
- }
-
- /**
- * Gets the value of the error property.
+ * @return possible object is {@link DbReferenceType }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getError() {
- return error;
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
}
/**
- * Sets the value of the error property.
+ * Sets the value of the dbReference property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link DbReferenceType }
+ *
*/
- public void setError(String value) {
- this.error = value;
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
}
/**
- * Gets the value of the method property.
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getMethod() {
- return method;
+ public String getId()
+ {
+ return id;
}
/**
- * Sets the value of the method property.
+ * Sets the value of the id property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setMethod(String value) {
- this.method = value;
+ 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="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "km", "vmax", "text" })
+ public static class Kinetics
+ {
+
+ @XmlElement(name = "KM")
+ protected List<EvidencedStringType> km;
+
+ @XmlElement(name = "Vmax")
+ protected List<EvidencedStringType> vmax;
+
+ protected List<EvidencedStringType> text;
+
/**
- * Gets the value of the evidence property.
+ * Gets the value of the km 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 evidence property.
+ * 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 km property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getEvidence().add(newItem);
+ * getKM().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Integer }
+ * {@link EvidencedStringType }
*
*
*/
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ public List<EvidencedStringType> getKM()
+ {
+ if (km == null)
+ {
+ km = new ArrayList<EvidencedStringType>();
+ }
+ return this.km;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the vmax property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 vmax property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getVmax().add(newItem);
* </pre>
*
*
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "max",
- "text"
- })
- public static class Absorption {
-
- protected EvidencedStringType max;
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setMax(EvidencedStringType value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the text 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 text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
- }
-
-
- /**
- * <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="sequence" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="resource" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="EMBL-CDS"/>
- * <enumeration value="EMBL"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="frameshift"/>
- * <enumeration value="erroneous initiation"/>
- * <enumeration value="erroneous termination"/>
- * <enumeration value="erroneous gene model prediction"/>
- * <enumeration value="erroneous translation"/>
- * <enumeration value="miscellaneous discrepancy"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "sequence"
- })
- public static class Conflict {
-
- protected CommentType.Conflict.Sequence sequence;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "ref")
- protected String ref;
-
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link CommentType.Conflict.Sequence }
- *
- */
- public CommentType.Conflict.Sequence getSequence() {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Conflict.Sequence }
- *
- */
- public void setSequence(CommentType.Conflict.Sequence value) {
- this.sequence = 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 ref property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRef() {
- return ref;
- }
-
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRef(String value) {
- this.ref = 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="resource" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="EMBL-CDS"/>
- * <enumeration value="EMBL"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Sequence {
-
- @XmlAttribute(name = "resource", required = true)
- protected String resource;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "version")
- protected Integer version;
-
- /**
- * Gets the value of the resource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getResource() {
- return resource;
- }
-
- /**
- * Sets the value of the resource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setResource(String value) {
- this.resource = 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 version property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setVersion(Integer value) {
- this.version = value;
- }
-
- }
-
+ public List<EvidencedStringType> getVmax()
+ {
+ if (vmax == null)
+ {
+ vmax = new ArrayList<EvidencedStringType>();
+ }
+ return this.vmax;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text 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 text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
- * </sequence>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "name",
- "acronym",
- "description",
- "dbReference"
- })
- public static class Disease {
-
- @XmlElement(required = true)
- protected String name;
- @XmlElement(required = true)
- protected String acronym;
- @XmlElement(required = true)
- protected String description;
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- /**
- * 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 acronym property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAcronym() {
- return acronym;
- }
-
- /**
- * Sets the value of the acronym property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAcronym(String value) {
- this.acronym = 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 dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
-
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = 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;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <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="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Link
+ {
+
+ @XmlAttribute(name = "uri", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected String uri;
/**
- * <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="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Gets the value of the uri property.
*
+ * @return possible object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "km",
- "vmax",
- "text"
- })
- public static class Kinetics {
-
- @XmlElement(name = "KM")
- protected List<EvidencedStringType> km;
- @XmlElement(name = "Vmax")
- protected List<EvidencedStringType> vmax;
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the km 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 km property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getKM().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getKM() {
- if (km == null) {
- km = new ArrayList<EvidencedStringType>();
- }
- return this.km;
- }
-
- /**
- * Gets the value of the vmax 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 vmax property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getVmax().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getVmax() {
- if (vmax == null) {
- vmax = new ArrayList<EvidencedStringType>();
- }
- return this.vmax;
- }
-
- /**
- * Gets the value of the text 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 text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public String getUri()
+ {
+ return uri;
}
-
/**
- * <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="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Sets the value of the uri property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Link {
-
- @XmlAttribute(name = "uri", required = true)
- @XmlSchemaType(name = "anyURI")
- protected String uri;
-
- /**
- * Gets the value of the uri property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getUri() {
- return uri;
- }
-
- /**
- * Sets the value of the uri property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setUri(String value) {
- this.uri = value;
- }
-
+ public void setUri(String value)
+ {
+ this.uri = 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="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "text" })
+ public static class PhDependence
+ {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text 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 text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "text"
- })
- public static class PhDependence {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the text 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 text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <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="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "text" })
+ public static class RedoxPotential
+ {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "text"
- })
- public static class RedoxPotential {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the text 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 text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <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="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "text" })
+ public static class TemperatureDependence
+ {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "text"
- })
- public static class TemperatureDependence {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the text 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 text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the authors of a citation when these are represented by a consortium.
- * Equivalent to the flat file RG-line.
+ * Describes the authors of a citation when these are represented by a
+ * consortium. Equivalent to the flat file RG-line.
*
- * <p>Java class for consortiumType complex type.
+ * <p>
+ * Java class for consortiumType 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="consortiumType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "consortiumType")
-public class ConsortiumType {
+public class ConsortiumType
+{
- @XmlAttribute(name = "name", required = true)
- protected String name;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a database cross-reference.
- * Equivalent to the flat file DR-line.
- *
+ * Describes a database cross-reference. Equivalent to the flat file DR-line.
*
- * <p>Java class for dbReferenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * Java class for dbReferenceType complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="dbReferenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "dbReferenceType", propOrder = {
- "molecule",
- "property"
-})
-public class DbReferenceType {
-
- protected MoleculeType molecule;
- protected List<PropertyType> property;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the molecule property.
- *
- * @return
- * possible object is
- * {@link MoleculeType }
- *
- */
- public MoleculeType getMolecule() {
- return molecule;
- }
+@XmlType(name = "dbReferenceType", propOrder = { "molecule", "property" })
+public class DbReferenceType
+{
- /**
- * Sets the value of the molecule property.
- *
- * @param value
- * allowed object is
- * {@link MoleculeType }
- *
- */
- public void setMolecule(MoleculeType value) {
- this.molecule = value;
- }
+ protected MoleculeType molecule;
- /**
- * 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 PropertyType }
- *
- *
- */
- public List<PropertyType> getProperty() {
- if (property == null) {
- property = new ArrayList<PropertyType>();
- }
- return this.property;
- }
+ protected List<PropertyType> property;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return possible object is {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule()
+ {
+ return molecule;
+ }
- /**
- * 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 molecule property.
+ *
+ * @param value
+ * allowed object is {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value)
+ {
+ this.molecule = 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 PropertyType }
+ *
+ *
+ */
+ public List<PropertyType> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<PropertyType>();
}
+ return this.property;
+ }
+
+ /**
+ * 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 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <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>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "accession",
- "name",
- "protein",
- "gene",
- "organism",
- "organismHost",
- "geneLocation",
- "reference",
- "comment",
- "dbReference",
- "proteinExistence",
- "keyword",
- "feature",
- "evidence",
- "sequence"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "accession", "name", "protein", "gene", "organism", "organismHost",
+ "geneLocation", "reference", "comment", "dbReference",
+ "proteinExistence", "keyword", "feature", "evidence", "sequence" })
@XmlRootElement(name = "entry")
-public class Entry {
-
- @XmlElement(required = true)
- protected List<String> accession;
- @XmlElement(required = true)
- protected List<String> name;
- @XmlElement(required = true)
- protected ProteinType protein;
- protected List<GeneType> gene;
- @XmlElement(required = true)
- protected OrganismType organism;
- protected List<OrganismType> organismHost;
- protected List<GeneLocationType> geneLocation;
- @XmlElement(required = true)
- protected List<ReferenceType> reference;
- @XmlElement(nillable = true)
- protected List<CommentType> comment;
- protected List<DbReferenceType> dbReference;
- @XmlElement(required = true)
- protected ProteinExistenceType proteinExistence;
- protected List<KeywordType> keyword;
- protected List<FeatureType> feature;
- protected List<EvidenceType> evidence;
- @XmlElement(required = true)
- protected SequenceType sequence;
- @XmlAttribute(name = "dataset", required = true)
- protected String dataset;
- @XmlAttribute(name = "created", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar created;
- @XmlAttribute(name = "modified", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar modified;
- @XmlAttribute(name = "version", required = true)
- protected int version;
-
- /**
- * Gets the value of the accession 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 accession property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAccession().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAccession() {
- if (accession == null) {
- accession = new ArrayList<String>();
- }
- return this.accession;
- }
+public class Entry
+{
- /**
- * Gets the value of the name 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 name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getName() {
- if (name == null) {
- name = new ArrayList<String>();
- }
- return this.name;
- }
+ @XmlElement(required = true)
+ protected List<String> accession;
- /**
- * Gets the value of the protein property.
- *
- * @return
- * possible object is
- * {@link ProteinType }
- *
- */
- public ProteinType getProtein() {
- return protein;
- }
+ @XmlElement(required = true)
+ protected List<String> name;
- /**
- * Sets the value of the protein property.
- *
- * @param value
- * allowed object is
- * {@link ProteinType }
- *
- */
- public void setProtein(ProteinType value) {
- this.protein = value;
- }
+ @XmlElement(required = true)
+ protected ProteinType protein;
- /**
- * Gets the value of the gene 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 gene property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getGene().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneType }
- *
- *
- */
- public List<GeneType> getGene() {
- if (gene == null) {
- gene = new ArrayList<GeneType>();
- }
- return this.gene;
- }
+ protected List<GeneType> gene;
- /**
- * Gets the value of the organism property.
- *
- * @return
- * possible object is
- * {@link OrganismType }
- *
- */
- public OrganismType getOrganism() {
- return organism;
- }
+ @XmlElement(required = true)
+ protected OrganismType organism;
- /**
- * Sets the value of the organism property.
- *
- * @param value
- * allowed object is
- * {@link OrganismType }
- *
- */
- public void setOrganism(OrganismType value) {
- this.organism = value;
- }
+ protected List<OrganismType> organismHost;
- /**
- * Gets the value of the organismHost 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 organismHost property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getOrganismHost().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link OrganismType }
- *
- *
- */
- public List<OrganismType> getOrganismHost() {
- if (organismHost == null) {
- organismHost = new ArrayList<OrganismType>();
- }
- return this.organismHost;
- }
+ protected List<GeneLocationType> geneLocation;
- /**
- * Gets the value of the geneLocation 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 geneLocation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getGeneLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneLocationType }
- *
- *
- */
- public List<GeneLocationType> getGeneLocation() {
- if (geneLocation == null) {
- geneLocation = new ArrayList<GeneLocationType>();
- }
- return this.geneLocation;
- }
+ @XmlElement(required = true)
+ protected List<ReferenceType> reference;
- /**
- * Gets the value of the reference 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 reference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ReferenceType }
- *
- *
- */
- public List<ReferenceType> getReference() {
- if (reference == null) {
- reference = new ArrayList<ReferenceType>();
- }
- return this.reference;
- }
+ @XmlElement(nillable = true)
+ protected List<CommentType> comment;
- /**
- * Gets the value of the comment 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 comment property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getComment().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CommentType }
- *
- *
- */
- public List<CommentType> getComment() {
- if (comment == null) {
- comment = new ArrayList<CommentType>();
- }
- return this.comment;
- }
+ protected List<DbReferenceType> dbReference;
- /**
- * Gets the value of the dbReference 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 dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
- }
+ @XmlElement(required = true)
+ protected ProteinExistenceType proteinExistence;
- /**
- * Gets the value of the proteinExistence property.
- *
- * @return
- * possible object is
- * {@link ProteinExistenceType }
- *
- */
- public ProteinExistenceType getProteinExistence() {
- return proteinExistence;
- }
+ protected List<KeywordType> keyword;
- /**
- * Sets the value of the proteinExistence property.
- *
- * @param value
- * allowed object is
- * {@link ProteinExistenceType }
- *
- */
- public void setProteinExistence(ProteinExistenceType value) {
- this.proteinExistence = value;
- }
+ protected List<FeatureType> feature;
- /**
- * Gets the value of the keyword 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 keyword property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getKeyword().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link KeywordType }
- *
- *
- */
- public List<KeywordType> getKeyword() {
- if (keyword == null) {
- keyword = new ArrayList<KeywordType>();
- }
- return this.keyword;
- }
+ protected List<EvidenceType> evidence;
- /**
- * Gets the value of the feature 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 feature property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getFeature().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link FeatureType }
- *
- *
- */
- public List<FeatureType> getFeature() {
- if (feature == null) {
- feature = new ArrayList<FeatureType>();
- }
- return this.feature;
- }
+ @XmlElement(required = true)
+ protected SequenceType sequence;
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidenceType }
- *
- *
- */
- public List<EvidenceType> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<EvidenceType>();
- }
- return this.evidence;
- }
+ @XmlAttribute(name = "dataset", required = true)
+ protected String dataset;
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link SequenceType }
- *
- */
- public SequenceType getSequence() {
- return sequence;
- }
+ @XmlAttribute(name = "created", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar created;
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link SequenceType }
- *
- */
- public void setSequence(SequenceType value) {
- this.sequence = value;
- }
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
- /**
- * Gets the value of the dataset property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDataset() {
- return dataset;
- }
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
- /**
- * Sets the value of the dataset property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDataset(String value) {
- this.dataset = value;
+ /**
+ * Gets the value of the accession 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 accession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getAccession()
+ {
+ if (accession == null)
+ {
+ accession = new ArrayList<String>();
}
-
- /**
- * Gets the value of the created property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreated() {
- return created;
+ return this.accession;
+ }
+
+ /**
+ * Gets the value of the name 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 name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<String>();
}
-
- /**
- * Sets the value of the created property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setCreated(XMLGregorianCalendar value) {
- this.created = value;
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the protein property.
+ *
+ * @return possible object is {@link ProteinType }
+ *
+ */
+ public ProteinType getProtein()
+ {
+ return protein;
+ }
+
+ /**
+ * Sets the value of the protein property.
+ *
+ * @param value
+ * allowed object is {@link ProteinType }
+ *
+ */
+ public void setProtein(ProteinType value)
+ {
+ this.protein = value;
+ }
+
+ /**
+ * Gets the value of the gene 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 gene property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getGene().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link GeneType }
+ *
+ *
+ */
+ public List<GeneType> getGene()
+ {
+ if (gene == null)
+ {
+ gene = new ArrayList<GeneType>();
}
-
- /**
- * Gets the value of the modified property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getModified() {
- return modified;
+ return this.gene;
+ }
+
+ /**
+ * Gets the value of the organism property.
+ *
+ * @return possible object is {@link OrganismType }
+ *
+ */
+ public OrganismType getOrganism()
+ {
+ return organism;
+ }
+
+ /**
+ * Sets the value of the organism property.
+ *
+ * @param value
+ * allowed object is {@link OrganismType }
+ *
+ */
+ public void setOrganism(OrganismType value)
+ {
+ this.organism = value;
+ }
+
+ /**
+ * Gets the value of the organismHost 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 organismHost property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getOrganismHost().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismType }
+ *
+ *
+ */
+ public List<OrganismType> getOrganismHost()
+ {
+ if (organismHost == null)
+ {
+ organismHost = new ArrayList<OrganismType>();
}
-
- /**
- * Sets the value of the modified property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setModified(XMLGregorianCalendar value) {
- this.modified = value;
+ return this.organismHost;
+ }
+
+ /**
+ * Gets the value of the geneLocation 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 geneLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getGeneLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneLocationType }
+ *
+ *
+ */
+ public List<GeneLocationType> getGeneLocation()
+ {
+ if (geneLocation == null)
+ {
+ geneLocation = new ArrayList<GeneLocationType>();
}
-
- /**
- * Gets the value of the version property.
- *
- */
- public int getVersion() {
- return version;
+ return this.geneLocation;
+ }
+
+ /**
+ * Gets the value of the reference 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 reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ReferenceType }
+ *
+ *
+ */
+ public List<ReferenceType> getReference()
+ {
+ if (reference == null)
+ {
+ reference = new ArrayList<ReferenceType>();
}
-
- /**
- * Sets the value of the version property.
- *
- */
- public void setVersion(int value) {
- this.version = value;
+ return this.reference;
+ }
+
+ /**
+ * Gets the value of the comment 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 comment property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getComment().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link CommentType
+ * }
+ *
+ *
+ */
+ public List<CommentType> getComment()
+ {
+ if (comment == null)
+ {
+ comment = new ArrayList<CommentType>();
+ }
+ return this.comment;
+ }
+
+ /**
+ * Gets the value of the dbReference 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 dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the proteinExistence property.
+ *
+ * @return possible object is {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType getProteinExistence()
+ {
+ return proteinExistence;
+ }
+
+ /**
+ * Sets the value of the proteinExistence property.
+ *
+ * @param value
+ * allowed object is {@link ProteinExistenceType }
+ *
+ */
+ public void setProteinExistence(ProteinExistenceType value)
+ {
+ this.proteinExistence = value;
+ }
+
+ /**
+ * Gets the value of the keyword 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 keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link KeywordType
+ * }
+ *
+ *
+ */
+ public List<KeywordType> getKeyword()
+ {
+ if (keyword == null)
+ {
+ keyword = new ArrayList<KeywordType>();
+ }
+ return this.keyword;
+ }
+
+ /**
+ * Gets the value of the feature 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 feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link FeatureType
+ * }
+ *
+ *
+ */
+ public List<FeatureType> getFeature()
+ {
+ if (feature == null)
+ {
+ feature = new ArrayList<FeatureType>();
+ }
+ return this.feature;
+ }
+
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidenceType }
+ *
+ *
+ */
+ public List<EvidenceType> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<EvidenceType>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link SequenceType }
+ *
+ */
+ public SequenceType getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link SequenceType }
+ *
+ */
+ public void setSequence(SequenceType value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the dataset property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDataset()
+ {
+ return dataset;
+ }
+
+ /**
+ * Sets the value of the dataset property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDataset(String value)
+ {
+ this.dataset = value;
+ }
+
+ /**
+ * Gets the value of the created property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreated()
+ {
+ return created;
+ }
+
+ /**
+ * Sets the value of the created property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreated(XMLGregorianCalendar value)
+ {
+ this.created = value;
+ }
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified()
+ {
+ return modified;
+ }
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value)
+ {
+ this.modified = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value)
+ {
+ this.version = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes the type of events that cause alternative products.
*
- * <p>Java class for eventType complex type.
+ * <p>
+ * Java class for eventType 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="eventType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "eventType")
-public class EventType {
+public class EventType
+{
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the evidence for an annotation.
- * No flat file equivalent.
+ * Describes the evidence for an annotation. No flat file equivalent.
*
- * <p>Java class for evidenceType complex type.
+ * <p>
+ * Java class for evidenceType 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="evidenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidenceType", propOrder = {
- "source",
- "importedFrom"
-})
-public class EvidenceType {
-
- protected SourceType source;
- protected ImportedFromType importedFrom;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "key", required = true)
- protected BigInteger key;
-
- /**
- * Gets the value of the source property.
- *
- * @return
- * possible object is
- * {@link SourceType }
- *
- */
- public SourceType getSource() {
- return source;
- }
-
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is
- * {@link SourceType }
- *
- */
- public void setSource(SourceType value) {
- this.source = value;
- }
-
- /**
- * Gets the value of the importedFrom property.
- *
- * @return
- * possible object is
- * {@link ImportedFromType }
- *
- */
- public ImportedFromType getImportedFrom() {
- return importedFrom;
- }
-
- /**
- * Sets the value of the importedFrom property.
- *
- * @param value
- * allowed object is
- * {@link ImportedFromType }
- *
- */
- public void setImportedFrom(ImportedFromType value) {
- this.importedFrom = 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 key property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getKey() {
- return key;
- }
-
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setKey(BigInteger value) {
- this.key = value;
- }
+@XmlType(name = "evidenceType", propOrder = { "source", "importedFrom" })
+public class EvidenceType
+{
+
+ protected SourceType source;
+
+ protected ImportedFromType importedFrom;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "key", required = true)
+ protected BigInteger key;
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return possible object is {@link SourceType }
+ *
+ */
+ public SourceType getSource()
+ {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is {@link SourceType }
+ *
+ */
+ public void setSource(SourceType value)
+ {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the importedFrom property.
+ *
+ * @return possible object is {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType getImportedFrom()
+ {
+ return importedFrom;
+ }
+
+ /**
+ * Sets the value of the importedFrom property.
+ *
+ * @param value
+ * allowed object is {@link ImportedFromType }
+ *
+ */
+ public void setImportedFrom(ImportedFromType value)
+ {
+ this.importedFrom = 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 key property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getKey()
+ {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setKey(BigInteger value)
+ {
+ this.key = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * <p>Java class for evidencedStringType complex type.
+ * <p>
+ * Java class for evidencedStringType 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="evidencedStringType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidencedStringType", propOrder = {
- "value"
-})
-public class EvidencedStringType {
+@XmlType(name = "evidencedStringType", propOrder = { "value" })
+public class EvidencedStringType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "status")
- protected String status;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
+ /**
+ * 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 status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes different types of sequence annotations.
- * Equivalent to the flat file FT-line.
+ * Describes different types of sequence annotations. Equivalent to the flat
+ * file FT-line.
*
- * <p>Java class for featureType complex type.
+ * <p>
+ * Java class for featureType 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="featureType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "featureType", propOrder = {
- "original",
- "variation",
- "location"
-})
-public class FeatureType {
+@XmlType(
+ name = "featureType",
+ propOrder =
+ { "original", "variation", "location" })
+public class FeatureType
+{
- protected String original;
- protected List<String> variation;
- @XmlElement(required = true)
- protected LocationType location;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "description")
- protected String description;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "ref")
- protected String ref;
+ protected String original;
- /**
- * Gets the value of the original property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getOriginal() {
- return original;
- }
+ protected List<String> variation;
- /**
- * Sets the value of the original property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setOriginal(String value) {
- this.original = value;
- }
+ @XmlElement(required = true)
+ protected LocationType location;
- /**
- * Gets the value of the variation 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 variation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getVariation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getVariation() {
- if (variation == null) {
- variation = new ArrayList<String>();
- }
- return this.variation;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the location property.
- *
- * @return
- * possible object is
- * {@link LocationType }
- *
- */
- public LocationType getLocation() {
- return location;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is
- * {@link LocationType }
- *
- */
- public void setLocation(LocationType value) {
- this.location = value;
- }
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "description")
+ protected String description;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
+ @XmlAttribute(name = "ref")
+ protected String ref;
- /**
- * 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 original property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getOriginal()
+ {
+ return original;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the original property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setOriginal(String value)
+ {
+ this.original = 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 variation 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 variation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getVariation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getVariation()
+ {
+ if (variation == null)
+ {
+ variation = new ArrayList<String>();
}
+ return this.variation;
+ }
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
+ /**
+ * Gets the value of the location property.
+ *
+ * @return possible object is {@link LocationType }
+ *
+ */
+ public LocationType getLocation()
+ {
+ return location;
+ }
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is {@link LocationType }
+ *
+ */
+ public void setLocation(LocationType value)
+ {
+ this.location = value;
+ }
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Gets the value of the ref property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRef() {
- return ref;
- }
+ /**
+ * 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 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;
+ }
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRef(String value) {
- this.ref = 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;
+ }
+
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getRef()
+ {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setRef(String value)
+ {
+ this.ref = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes non-nuclear gene locations (organelles and plasmids).
- * Equivalent to the flat file OG-line.
+ * Describes non-nuclear gene locations (organelles and plasmids). Equivalent to
+ * the flat file OG-line.
*
- * <p>Java class for geneLocationType complex type.
+ * <p>
+ * Java class for geneLocationType 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="geneLocationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneLocationType", propOrder = {
- "name"
-})
-public class GeneLocationType {
+@XmlType(name = "geneLocationType", propOrder = { "name" })
+public class GeneLocationType
+{
- protected List<StatusType> name;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ protected List<StatusType> name;
- /**
- * Gets the value of the name 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 name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link StatusType }
- *
- *
- */
- public List<StatusType> getName() {
- if (name == null) {
- name = new ArrayList<StatusType>();
- }
- return this.name;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * 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 name 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 name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link StatusType
+ * }
+ *
+ *
+ */
+ public List<StatusType> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<StatusType>();
}
+ return this.name;
+ }
+
+ /**
+ * 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * Describes different types of gene designations.
- * Equivalent to the flat file GN-line.
+ * Describes different types of gene designations. Equivalent to the flat file
+ * GN-line.
*
- * <p>Java class for geneNameType complex type.
+ * <p>
+ * Java class for geneNameType 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="geneNameType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneNameType", propOrder = {
- "value"
-})
-public class GeneNameType {
+@XmlType(name = "geneNameType", propOrder = { "value" })
+public class GeneNameType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * 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 type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a gene.
- * Equivalent to the flat file GN-line.
+ * Describes a gene. Equivalent to the flat file GN-line.
*
- * <p>Java class for geneType complex type.
+ * <p>
+ * Java class for geneType 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="geneType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneType", propOrder = {
- "name"
-})
-public class GeneType {
+@XmlType(name = "geneType", propOrder = { "name" })
+public class GeneType
+{
- @XmlElement(required = true)
- protected List<GeneNameType> name;
+ @XmlElement(required = true)
+ protected List<GeneNameType> name;
- /**
- * Gets the value of the name 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 name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneNameType }
- *
- *
- */
- public List<GeneNameType> getName() {
- if (name == null) {
- name = new ArrayList<GeneNameType>();
- }
- return this.name;
+ /**
+ * Gets the value of the name 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 name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneNameType }
+ *
+ *
+ */
+ public List<GeneNameType> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<GeneNameType>();
}
+ return this.name;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
+ * Describes the source of the evidence, when it is not assigned by UniProt, but
+ * imported from an external database.
*
- * <p>Java class for importedFromType complex type.
+ * <p>
+ * Java class for importedFromType 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="importedFromType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "importedFromType", propOrder = {
- "dbReference"
-})
-public class ImportedFromType {
+@XmlType(name = "importedFromType", propOrder = { "dbReference" })
+public class ImportedFromType
+{
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for interactantType complex type.
+ * <p>
+ * Java class for interactantType 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="interactantType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "interactantType", propOrder = {
- "id",
- "label"
-})
-public class InteractantType {
+@XmlType(name = "interactantType", propOrder = { "id", "label" })
+public class InteractantType
+{
+
+ protected String id;
+
+ protected String label;
- protected String id;
- protected String label;
- @XmlAttribute(name = "intactId", required = true)
- protected String intactId;
+ @XmlAttribute(name = "intactId", required = true)
+ protected String intactId;
- /**
- * 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 label property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLabel() {
- return 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;
- }
+ /**
+ * 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 intactId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getIntactId() {
- return intactId;
- }
+ /**
+ * Gets the value of the intactId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getIntactId()
+ {
+ return intactId;
+ }
- /**
- * Sets the value of the intactId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setIntactId(String value) {
- this.intactId = value;
- }
+ /**
+ * Sets the value of the intactId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setIntactId(String value)
+ {
+ this.intactId = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Describes isoforms in 'alternative products' annotations.
*
- * <p>Java class for isoformType complex type.
+ * <p>
+ * Java class for isoformType 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="isoformType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "isoformType", propOrder = {
- "id",
- "name",
- "sequence",
- "text"
-})
-public class IsoformType {
+@XmlType(
+ name = "isoformType",
+ propOrder =
+ { "id", "name", "sequence", "text" })
+public class IsoformType
+{
- @XmlElement(required = true)
- protected List<String> id;
- @XmlElement(required = true)
- protected List<IsoformType.Name> name;
- @XmlElement(required = true)
- protected IsoformType.Sequence sequence;
- protected List<EvidencedStringType> text;
+ @XmlElement(required = true)
+ protected List<String> id;
- /**
- * Gets the value of the id 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 id property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getId().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getId() {
- if (id == null) {
- id = new ArrayList<String>();
- }
- return this.id;
+ @XmlElement(required = true)
+ protected List<IsoformType.Name> name;
+
+ @XmlElement(required = true)
+ protected IsoformType.Sequence sequence;
+
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the id 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 id property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getId().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getId()
+ {
+ if (id == null)
+ {
+ id = new ArrayList<String>();
}
+ return this.id;
+ }
- /**
- * Gets the value of the name 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 name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link IsoformType.Name }
- *
- *
- */
- public List<IsoformType.Name> getName() {
- if (name == null) {
- name = new ArrayList<IsoformType.Name>();
- }
- return this.name;
+ /**
+ * Gets the value of the name 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 name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link IsoformType.Name }
+ *
+ *
+ */
+ public List<IsoformType.Name> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<IsoformType.Name>();
+ }
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link IsoformType.Sequence }
+ *
+ */
+ public IsoformType.Sequence getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link IsoformType.Sequence }
+ *
+ */
+ public void setSequence(IsoformType.Sequence value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the text 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 text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
}
+ return this.text;
+ }
+
+ /**
+ * <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">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Name
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
/**
- * Gets the value of the sequence property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link IsoformType.Sequence }
- *
*/
- public IsoformType.Sequence getSequence() {
- return sequence;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the sequence property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link IsoformType.Sequence }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setSequence(IsoformType.Sequence value) {
- this.sequence = value;
+ public void setValue(String value)
+ {
+ this.value = value;
}
/**
- * Gets the value of the text property.
+ * Gets the value of the evidence 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 text property.
+ * 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 evidence property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getText().add(newItem);
+ * getEvidence().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
+ * Objects of the following type(s) are allowed in the list {@link Integer }
*
*
*/
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
+ }
+
+ /**
+ * <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="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="not described"/>
+ * <enumeration value="described"/>
+ * <enumeration value="displayed"/>
+ * <enumeration value="external"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence
+ {
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "ref")
+ protected String ref;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the type property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Name {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
-
+ public void setType(String value)
+ {
+ this.type = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the ref property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="not described"/>
- * <enumeration value="described"/>
- * <enumeration value="displayed"/>
- * <enumeration value="external"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getRef()
+ {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Sequence {
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "ref")
- protected String ref;
-
- /**
- * 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 ref property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRef() {
- return ref;
- }
-
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRef(String value) {
- this.ref = value;
- }
-
+ public void setRef(String value)
+ {
+ this.ref = value;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * <p>Java class for keywordType complex type.
+ * <p>
+ * Java class for keywordType 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="keywordType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "keywordType", propOrder = {
- "value"
-})
-public class KeywordType {
+@XmlType(name = "keywordType", propOrder = { "value" })
+public class KeywordType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "id", required = true)
- protected String id;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * 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 id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
+ * Describes a sequence location as either a range with a begin and end or as a
+ * position. The 'sequence' attribute is only used when the location is not on
+ * the canonical sequence displayed in the current entry.
*
- * <p>Java class for locationType complex type.
+ * <p>
+ * Java class for locationType 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="locationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "locationType", propOrder = {
- "begin",
- "end",
- "position"
-})
-public class LocationType {
-
- protected PositionType begin;
- protected PositionType end;
- protected PositionType position;
- @XmlAttribute(name = "sequence")
- protected String sequence;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link PositionType }
- *
- */
- public PositionType getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link PositionType }
- *
- */
- public void setBegin(PositionType value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link PositionType }
- *
- */
- public PositionType getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link PositionType }
- *
- */
- public void setEnd(PositionType value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- * @return
- * possible object is
- * {@link PositionType }
- *
- */
- public PositionType getPosition() {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is
- * {@link PositionType }
- *
- */
- public void setPosition(PositionType value) {
- this.position = value;
- }
-
- /**
- * 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;
- }
+@XmlType(name = "locationType", propOrder = { "begin", "end", "position" })
+public class LocationType
+{
+
+ protected PositionType begin;
+
+ protected PositionType end;
+
+ protected PositionType position;
+
+ @XmlAttribute(name = "sequence")
+ protected String sequence;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link PositionType }
+ *
+ */
+ public PositionType getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link PositionType }
+ *
+ */
+ public void setBegin(PositionType value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link PositionType }
+ *
+ */
+ public PositionType getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link PositionType }
+ *
+ */
+ public void setEnd(PositionType value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ * @return possible object is {@link PositionType }
+ *
+ */
+ public PositionType getPosition()
+ {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is {@link PositionType }
+ *
+ */
+ public void setPosition(PositionType value)
+ {
+ this.position = value;
+ }
+
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Describes a molecule by name or unique identifier.
*
- * <p>Java class for moleculeType complex type.
+ * <p>
+ * Java class for moleculeType 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="moleculeType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "moleculeType", propOrder = {
- "value"
-})
-public class MoleculeType {
+@XmlType(name = "moleculeType", propOrder = { "value" })
+public class MoleculeType
+{
+
+ @XmlValue
+ protected String value;
- @XmlValue
- protected String value;
- @XmlAttribute(name = "id")
- protected String id;
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * 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 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElements;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for nameListType complex type.
+ * <p>
+ * Java class for nameListType 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="nameListType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "nameListType", propOrder = {
- "consortiumOrPerson"
-})
-public class NameListType {
+@XmlType(name = "nameListType", propOrder = { "consortiumOrPerson" })
+public class NameListType
+{
- @XmlElements({
- @XmlElement(name = "consortium", type = ConsortiumType.class),
- @XmlElement(name = "person", type = PersonType.class)
- })
- protected List<Object> consortiumOrPerson;
+ @XmlElements({
+ @XmlElement(name = "consortium", type = ConsortiumType.class),
+ @XmlElement(name = "person", type = PersonType.class) })
+ protected List<Object> consortiumOrPerson;
- /**
- * Gets the value of the consortiumOrPerson 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 consortiumOrPerson property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getConsortiumOrPerson().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ConsortiumType }
- * {@link PersonType }
- *
- *
- */
- public List<Object> getConsortiumOrPerson() {
- if (consortiumOrPerson == null) {
- consortiumOrPerson = new ArrayList<Object>();
- }
- return this.consortiumOrPerson;
+ /**
+ * Gets the value of the consortiumOrPerson 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 consortiumOrPerson property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getConsortiumOrPerson().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ConsortiumType } {@link PersonType }
+ *
+ *
+ */
+ public List<Object> getConsortiumOrPerson()
+ {
+ if (consortiumOrPerson == null)
+ {
+ consortiumOrPerson = new ArrayList<Object>();
}
+ return this.consortiumOrPerson;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
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.uniprot 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.uniprot 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 _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link SourceDataType }
- *
- */
- public SourceDataType createSourceDataType() {
- return new SourceDataType();
- }
-
- /**
- * Create an instance of {@link IsoformType }
- *
- */
- public IsoformType createIsoformType() {
- return new IsoformType();
- }
-
- /**
- * Create an instance of {@link CommentType }
- *
- */
- public CommentType createCommentType() {
- return new CommentType();
- }
-
- /**
- * Create an instance of {@link CommentType.Conflict }
- *
- */
- public CommentType.Conflict createCommentTypeConflict() {
- return new CommentType.Conflict();
- }
-
- /**
- * Create an instance of {@link OrganismType }
- *
- */
- public OrganismType createOrganismType() {
- return new OrganismType();
- }
-
- /**
- * Create an instance of {@link ProteinType }
- *
- */
- public ProteinType createProteinType() {
- return new ProteinType();
- }
-
- /**
- * Create an instance of {@link Entry }
- *
- */
- public Entry createEntry() {
- return new Entry();
- }
-
- /**
- * Create an instance of {@link GeneType }
- *
- */
- public GeneType createGeneType() {
- return new GeneType();
- }
-
- /**
- * Create an instance of {@link GeneLocationType }
- *
- */
- public GeneLocationType createGeneLocationType() {
- return new GeneLocationType();
- }
-
- /**
- * Create an instance of {@link ReferenceType }
- *
- */
- public ReferenceType createReferenceType() {
- return new ReferenceType();
- }
-
- /**
- * Create an instance of {@link DbReferenceType }
- *
- */
- public DbReferenceType createDbReferenceType() {
- return new DbReferenceType();
- }
-
- /**
- * Create an instance of {@link ProteinExistenceType }
- *
- */
- public ProteinExistenceType createProteinExistenceType() {
- return new ProteinExistenceType();
- }
-
- /**
- * Create an instance of {@link KeywordType }
- *
- */
- public KeywordType createKeywordType() {
- return new KeywordType();
- }
-
- /**
- * Create an instance of {@link FeatureType }
- *
- */
- public FeatureType createFeatureType() {
- return new FeatureType();
- }
-
- /**
- * Create an instance of {@link EvidenceType }
- *
- */
- public EvidenceType createEvidenceType() {
- return new EvidenceType();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType() {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Uniprot }
- *
- */
- public Uniprot createUniprot() {
- return new Uniprot();
- }
-
- /**
- * Create an instance of {@link StatusType }
- *
- */
- public StatusType createStatusType() {
- return new StatusType();
- }
-
- /**
- * Create an instance of {@link PositionType }
- *
- */
- public PositionType createPositionType() {
- return new PositionType();
- }
-
- /**
- * Create an instance of {@link ConsortiumType }
- *
- */
- public ConsortiumType createConsortiumType() {
- return new ConsortiumType();
- }
-
- /**
- * Create an instance of {@link GeneNameType }
- *
- */
- public GeneNameType createGeneNameType() {
- return new GeneNameType();
- }
-
- /**
- * Create an instance of {@link LocationType }
- *
- */
- public LocationType createLocationType() {
- return new LocationType();
- }
-
- /**
- * Create an instance of {@link CitationType }
- *
- */
- public CitationType createCitationType() {
- return new CitationType();
- }
-
- /**
- * Create an instance of {@link PropertyType }
- *
- */
- public PropertyType createPropertyType() {
- return new PropertyType();
- }
-
- /**
- * Create an instance of {@link PhysiologicalReactionType }
- *
- */
- public PhysiologicalReactionType createPhysiologicalReactionType() {
- return new PhysiologicalReactionType();
- }
-
- /**
- * Create an instance of {@link CofactorType }
- *
- */
- public CofactorType createCofactorType() {
- return new CofactorType();
- }
-
- /**
- * Create an instance of {@link EvidencedStringType }
- *
- */
- public EvidencedStringType createEvidencedStringType() {
- return new EvidencedStringType();
- }
-
- /**
- * Create an instance of {@link PersonType }
- *
- */
- public PersonType createPersonType() {
- return new PersonType();
- }
-
- /**
- * Create an instance of {@link ImportedFromType }
- *
- */
- public ImportedFromType createImportedFromType() {
- return new ImportedFromType();
- }
-
- /**
- * Create an instance of {@link EventType }
- *
- */
- public EventType createEventType() {
- return new EventType();
- }
-
- /**
- * Create an instance of {@link InteractantType }
- *
- */
- public InteractantType createInteractantType() {
- return new InteractantType();
- }
-
- /**
- * Create an instance of {@link NameListType }
- *
- */
- public NameListType createNameListType() {
- return new NameListType();
- }
-
- /**
- * Create an instance of {@link ReactionType }
- *
- */
- public ReactionType createReactionType() {
- return new ReactionType();
- }
-
- /**
- * Create an instance of {@link SourceType }
- *
- */
- public SourceType createSourceType() {
- return new SourceType();
- }
-
- /**
- * Create an instance of {@link MoleculeType }
- *
- */
- public MoleculeType createMoleculeType() {
- return new MoleculeType();
- }
-
- /**
- * Create an instance of {@link OrganismNameType }
- *
- */
- public OrganismNameType createOrganismNameType() {
- return new OrganismNameType();
- }
-
- /**
- * Create an instance of {@link SubcellularLocationType }
- *
- */
- public SubcellularLocationType createSubcellularLocationType() {
- return new SubcellularLocationType();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Strain }
- *
- */
- public SourceDataType.Strain createSourceDataTypeStrain() {
- return new SourceDataType.Strain();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Plasmid }
- *
- */
- public SourceDataType.Plasmid createSourceDataTypePlasmid() {
- return new SourceDataType.Plasmid();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Transposon }
- *
- */
- public SourceDataType.Transposon createSourceDataTypeTransposon() {
- return new SourceDataType.Transposon();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Tissue }
- *
- */
- public SourceDataType.Tissue createSourceDataTypeTissue() {
- return new SourceDataType.Tissue();
- }
-
- /**
- * Create an instance of {@link IsoformType.Name }
- *
- */
- public IsoformType.Name createIsoformTypeName() {
- return new IsoformType.Name();
- }
-
- /**
- * Create an instance of {@link IsoformType.Sequence }
- *
- */
- public IsoformType.Sequence createIsoformTypeSequence() {
- return new IsoformType.Sequence();
- }
-
- /**
- * Create an instance of {@link CommentType.Absorption }
- *
- */
- public CommentType.Absorption createCommentTypeAbsorption() {
- return new CommentType.Absorption();
- }
-
- /**
- * Create an instance of {@link CommentType.Kinetics }
- *
- */
- public CommentType.Kinetics createCommentTypeKinetics() {
- return new CommentType.Kinetics();
- }
-
- /**
- * Create an instance of {@link CommentType.PhDependence }
- *
- */
- public CommentType.PhDependence createCommentTypePhDependence() {
- return new CommentType.PhDependence();
- }
-
- /**
- * Create an instance of {@link CommentType.RedoxPotential }
- *
- */
- public CommentType.RedoxPotential createCommentTypeRedoxPotential() {
- return new CommentType.RedoxPotential();
- }
-
- /**
- * Create an instance of {@link CommentType.TemperatureDependence }
- *
- */
- public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() {
- return new CommentType.TemperatureDependence();
- }
-
- /**
- * Create an instance of {@link CommentType.Link }
- *
- */
- public CommentType.Link createCommentTypeLink() {
- return new CommentType.Link();
- }
-
- /**
- * Create an instance of {@link CommentType.Disease }
- *
- */
- public CommentType.Disease createCommentTypeDisease() {
- return new CommentType.Disease();
- }
-
- /**
- * Create an instance of {@link CommentType.Conflict.Sequence }
- *
- */
- public CommentType.Conflict.Sequence createCommentTypeConflictSequence() {
- return new CommentType.Conflict.Sequence();
- }
-
- /**
- * Create an instance of {@link OrganismType.Lineage }
- *
- */
- public OrganismType.Lineage createOrganismTypeLineage() {
- return new OrganismType.Lineage();
- }
-
- /**
- * Create an instance of {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName createProteinTypeRecommendedName() {
- return new ProteinType.RecommendedName();
- }
-
- /**
- * Create an instance of {@link ProteinType.AlternativeName }
- *
- */
- public ProteinType.AlternativeName createProteinTypeAlternativeName() {
- return new ProteinType.AlternativeName();
- }
-
- /**
- * Create an instance of {@link ProteinType.SubmittedName }
- *
- */
- public ProteinType.SubmittedName createProteinTypeSubmittedName() {
- return new ProteinType.SubmittedName();
- }
-
- /**
- * Create an instance of {@link ProteinType.Domain }
- *
- */
- public ProteinType.Domain createProteinTypeDomain() {
- return new ProteinType.Domain();
- }
-
- /**
- * Create an instance of {@link ProteinType.Component }
- *
- */
- public ProteinType.Component createProteinTypeComponent() {
- return new ProteinType.Component();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
- public JAXBElement<String> createCopyright(String value) {
- return new JAXBElement<String>(_Copyright_QNAME, String.class, null, value);
- }
+public class ObjectFactory
+{
+
+ private final static QName _Copyright_QNAME = new QName(
+ "http://uniprot.org/uniprot", "copyright");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.uniprot
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType }
+ *
+ */
+ public SourceDataType createSourceDataType()
+ {
+ return new SourceDataType();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType }
+ *
+ */
+ public IsoformType createIsoformType()
+ {
+ return new IsoformType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType }
+ *
+ */
+ public CommentType createCommentType()
+ {
+ return new CommentType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict }
+ *
+ */
+ public CommentType.Conflict createCommentTypeConflict()
+ {
+ return new CommentType.Conflict();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType }
+ *
+ */
+ public OrganismType createOrganismType()
+ {
+ return new OrganismType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType }
+ *
+ */
+ public ProteinType createProteinType()
+ {
+ return new ProteinType();
+ }
+
+ /**
+ * Create an instance of {@link Entry }
+ *
+ */
+ public Entry createEntry()
+ {
+ return new Entry();
+ }
+
+ /**
+ * Create an instance of {@link GeneType }
+ *
+ */
+ public GeneType createGeneType()
+ {
+ return new GeneType();
+ }
+
+ /**
+ * Create an instance of {@link GeneLocationType }
+ *
+ */
+ public GeneLocationType createGeneLocationType()
+ {
+ return new GeneLocationType();
+ }
+
+ /**
+ * Create an instance of {@link ReferenceType }
+ *
+ */
+ public ReferenceType createReferenceType()
+ {
+ return new ReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType createDbReferenceType()
+ {
+ return new DbReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType createProteinExistenceType()
+ {
+ return new ProteinExistenceType();
+ }
+
+ /**
+ * Create an instance of {@link KeywordType }
+ *
+ */
+ public KeywordType createKeywordType()
+ {
+ return new KeywordType();
+ }
+
+ /**
+ * Create an instance of {@link FeatureType }
+ *
+ */
+ public FeatureType createFeatureType()
+ {
+ return new FeatureType();
+ }
+
+ /**
+ * Create an instance of {@link EvidenceType }
+ *
+ */
+ public EvidenceType createEvidenceType()
+ {
+ return new EvidenceType();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType()
+ {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Uniprot }
+ *
+ */
+ public Uniprot createUniprot()
+ {
+ return new Uniprot();
+ }
+
+ /**
+ * Create an instance of {@link StatusType }
+ *
+ */
+ public StatusType createStatusType()
+ {
+ return new StatusType();
+ }
+
+ /**
+ * Create an instance of {@link PositionType }
+ *
+ */
+ public PositionType createPositionType()
+ {
+ return new PositionType();
+ }
+
+ /**
+ * Create an instance of {@link ConsortiumType }
+ *
+ */
+ public ConsortiumType createConsortiumType()
+ {
+ return new ConsortiumType();
+ }
+
+ /**
+ * Create an instance of {@link GeneNameType }
+ *
+ */
+ public GeneNameType createGeneNameType()
+ {
+ return new GeneNameType();
+ }
+
+ /**
+ * Create an instance of {@link LocationType }
+ *
+ */
+ public LocationType createLocationType()
+ {
+ return new LocationType();
+ }
+
+ /**
+ * Create an instance of {@link CitationType }
+ *
+ */
+ public CitationType createCitationType()
+ {
+ return new CitationType();
+ }
+
+ /**
+ * Create an instance of {@link PropertyType }
+ *
+ */
+ public PropertyType createPropertyType()
+ {
+ return new PropertyType();
+ }
+
+ /**
+ * Create an instance of {@link PhysiologicalReactionType }
+ *
+ */
+ public PhysiologicalReactionType createPhysiologicalReactionType()
+ {
+ return new PhysiologicalReactionType();
+ }
+
+ /**
+ * Create an instance of {@link CofactorType }
+ *
+ */
+ public CofactorType createCofactorType()
+ {
+ return new CofactorType();
+ }
+
+ /**
+ * Create an instance of {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType createEvidencedStringType()
+ {
+ return new EvidencedStringType();
+ }
+
+ /**
+ * Create an instance of {@link PersonType }
+ *
+ */
+ public PersonType createPersonType()
+ {
+ return new PersonType();
+ }
+
+ /**
+ * Create an instance of {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType createImportedFromType()
+ {
+ return new ImportedFromType();
+ }
+
+ /**
+ * Create an instance of {@link EventType }
+ *
+ */
+ public EventType createEventType()
+ {
+ return new EventType();
+ }
+
+ /**
+ * Create an instance of {@link InteractantType }
+ *
+ */
+ public InteractantType createInteractantType()
+ {
+ return new InteractantType();
+ }
+
+ /**
+ * Create an instance of {@link NameListType }
+ *
+ */
+ public NameListType createNameListType()
+ {
+ return new NameListType();
+ }
+
+ /**
+ * Create an instance of {@link ReactionType }
+ *
+ */
+ public ReactionType createReactionType()
+ {
+ return new ReactionType();
+ }
+
+ /**
+ * Create an instance of {@link SourceType }
+ *
+ */
+ public SourceType createSourceType()
+ {
+ return new SourceType();
+ }
+
+ /**
+ * Create an instance of {@link MoleculeType }
+ *
+ */
+ public MoleculeType createMoleculeType()
+ {
+ return new MoleculeType();
+ }
+
+ /**
+ * Create an instance of {@link OrganismNameType }
+ *
+ */
+ public OrganismNameType createOrganismNameType()
+ {
+ return new OrganismNameType();
+ }
+
+ /**
+ * Create an instance of {@link SubcellularLocationType }
+ *
+ */
+ public SubcellularLocationType createSubcellularLocationType()
+ {
+ return new SubcellularLocationType();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Strain }
+ *
+ */
+ public SourceDataType.Strain createSourceDataTypeStrain()
+ {
+ return new SourceDataType.Strain();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Plasmid }
+ *
+ */
+ public SourceDataType.Plasmid createSourceDataTypePlasmid()
+ {
+ return new SourceDataType.Plasmid();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Transposon }
+ *
+ */
+ public SourceDataType.Transposon createSourceDataTypeTransposon()
+ {
+ return new SourceDataType.Transposon();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Tissue }
+ *
+ */
+ public SourceDataType.Tissue createSourceDataTypeTissue()
+ {
+ return new SourceDataType.Tissue();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Name }
+ *
+ */
+ public IsoformType.Name createIsoformTypeName()
+ {
+ return new IsoformType.Name();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Sequence }
+ *
+ */
+ public IsoformType.Sequence createIsoformTypeSequence()
+ {
+ return new IsoformType.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption createCommentTypeAbsorption()
+ {
+ return new CommentType.Absorption();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics createCommentTypeKinetics()
+ {
+ return new CommentType.Kinetics();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence createCommentTypePhDependence()
+ {
+ return new CommentType.PhDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential createCommentTypeRedoxPotential()
+ {
+ return new CommentType.RedoxPotential();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence createCommentTypeTemperatureDependence()
+ {
+ return new CommentType.TemperatureDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Link }
+ *
+ */
+ public CommentType.Link createCommentTypeLink()
+ {
+ return new CommentType.Link();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Disease }
+ *
+ */
+ public CommentType.Disease createCommentTypeDisease()
+ {
+ return new CommentType.Disease();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public CommentType.Conflict.Sequence createCommentTypeConflictSequence()
+ {
+ return new CommentType.Conflict.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage createOrganismTypeLineage()
+ {
+ return new OrganismType.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName createProteinTypeRecommendedName()
+ {
+ return new ProteinType.RecommendedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.AlternativeName }
+ *
+ */
+ public ProteinType.AlternativeName createProteinTypeAlternativeName()
+ {
+ return new ProteinType.AlternativeName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.SubmittedName }
+ *
+ */
+ public ProteinType.SubmittedName createProteinTypeSubmittedName()
+ {
+ return new ProteinType.SubmittedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Domain }
+ *
+ */
+ public ProteinType.Domain createProteinTypeDomain()
+ {
+ return new ProteinType.Domain();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Component }
+ *
+ */
+ public ProteinType.Component createProteinTypeComponent()
+ {
+ return new ProteinType.Component();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link String
+ * }{@code >}}
+ *
+ */
+ @XmlElementDecl(
+ namespace = "http://uniprot.org/uniprot",
+ name = "copyright")
+ public JAXBElement<String> createCopyright(String value)
+ {
+ return new JAXBElement<String>(_Copyright_QNAME, String.class, null,
+ value);
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Describes different types of source organism names.
*
- * <p>Java class for organismNameType complex type.
+ * <p>
+ * Java class for organismNameType 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="organismNameType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismNameType", propOrder = {
- "value"
-})
-public class OrganismNameType {
+@XmlType(name = "organismNameType", propOrder = { "value" })
+public class OrganismNameType
+{
+
+ @XmlValue
+ protected String value;
- @XmlValue
- protected String value;
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * 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 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes the source organism.
*
- * <p>Java class for organismType complex type.
+ * <p>
+ * Java class for organismType 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="organismType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismType", propOrder = {
- "name",
- "dbReference",
- "lineage"
-})
-public class OrganismType {
-
- @XmlElement(required = true)
- protected List<OrganismNameType> name;
- @XmlElement(required = true)
- protected List<DbReferenceType> dbReference;
- protected OrganismType.Lineage lineage;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the name 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 name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link OrganismNameType }
- *
- *
- */
- public List<OrganismNameType> getName() {
- if (name == null) {
- name = new ArrayList<OrganismNameType>();
- }
- return this.name;
+@XmlType(
+ name = "organismType",
+ propOrder =
+ { "name", "dbReference", "lineage" })
+public class OrganismType
+{
+
+ @XmlElement(required = true)
+ protected List<OrganismNameType> name;
+
+ @XmlElement(required = true)
+ protected List<DbReferenceType> dbReference;
+
+ protected OrganismType.Lineage lineage;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the name 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 name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismNameType }
+ *
+ *
+ */
+ public List<OrganismNameType> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<OrganismNameType>();
}
-
- /**
- * Gets the value of the dbReference 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 dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the dbReference 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 dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
}
-
- /**
- * Gets the value of the lineage property.
- *
- * @return
- * possible object is
- * {@link OrganismType.Lineage }
- *
- */
- public OrganismType.Lineage getLineage() {
- return lineage;
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return possible object is {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage getLineage()
+ {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is {@link OrganismType.Lineage }
+ *
+ */
+ public void setLineage(OrganismType.Lineage value)
+ {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * <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="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "taxon" })
+ public static class Lineage
+ {
- /**
- * Sets the value of the lineage property.
- *
- * @param value
- * allowed object is
- * {@link OrganismType.Lineage }
- *
- */
- public void setLineage(OrganismType.Lineage value) {
- this.lineage = value;
- }
+ @XmlElement(required = true)
+ protected List<String> taxon;
/**
- * Gets the value of the evidence property.
+ * Gets the value of the taxon 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 evidence property.
+ * 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 taxon property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getEvidence().add(newItem);
+ * getTaxon().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
+ * Objects of the following type(s) are allowed in the list {@link String }
*
*
*/
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ public List<String> getTaxon()
+ {
+ if (taxon == null)
+ {
+ taxon = new ArrayList<String>();
+ }
+ return this.taxon;
}
-
- /**
- * <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="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "taxon"
- })
- public static class Lineage {
-
- @XmlElement(required = true)
- protected List<String> taxon;
-
- /**
- * Gets the value of the taxon 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 taxon property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTaxon().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getTaxon() {
- if (taxon == null) {
- taxon = new ArrayList<String>();
- }
- return this.taxon;
- }
-
- }
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for personType complex type.
+ * <p>
+ * Java class for personType 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="personType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "personType")
-public class PersonType {
+public class PersonType
+{
- @XmlAttribute(name = "name", required = true)
- protected String name;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes a physiological reaction.
*
- * <p>Java class for physiologicalReactionType complex type.
+ * <p>
+ * Java class for physiologicalReactionType 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="physiologicalReactionType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "physiologicalReactionType", propOrder = {
- "dbReference"
-})
-public class PhysiologicalReactionType {
+@XmlType(name = "physiologicalReactionType", propOrder = { "dbReference" })
+public class PhysiologicalReactionType
+{
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "direction", required = true)
- protected String direction;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ @XmlAttribute(name = "direction", required = true)
+ protected String direction;
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the direction property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDirection() {
- return direction;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
- /**
- * Sets the value of the direction property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDirection(String value) {
- this.direction = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
+
+ /**
+ * Gets the value of the direction property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDirection()
+ {
+ return direction;
+ }
+
+ /**
+ * Sets the value of the direction property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDirection(String value)
+ {
+ this.direction = value;
+ }
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for positionType complex type.
+ * <p>
+ * Java class for positionType 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="positionType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "positionType")
-public class PositionType {
+public class PositionType
+{
- @XmlAttribute(name = "position")
- @XmlSchemaType(name = "unsignedLong")
- protected BigInteger position;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlAttribute(name = "position")
+ @XmlSchemaType(name = "unsignedLong")
+ protected BigInteger position;
- /**
- * Gets the value of the position property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPosition() {
- return position;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPosition(BigInteger value) {
- this.position = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- if (status == null) {
- return "certain";
- } else {
- return status;
- }
- }
+ /**
+ * Gets the value of the position property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPosition()
+ {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPosition(BigInteger value)
+ {
+ this.position = value;
+ }
- /**
- * 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 status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ if (status == null)
+ {
+ return "certain";
}
+ else
+ {
+ 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for propertyType complex type.
+ * <p>
+ * Java class for propertyType 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="propertyType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "propertyType")
-public class PropertyType {
+public class PropertyType
+{
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "value", required = true)
- protected String value;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
- /**
- * 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 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the evidence for the protein's existence.
- * Equivalent to the flat file PE-line.
+ * Describes the evidence for the protein's existence. Equivalent to the flat
+ * file PE-line.
*
- * <p>Java class for proteinExistenceType complex type.
+ * <p>
+ * Java class for proteinExistenceType 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="proteinExistenceType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "proteinExistenceType")
-public class ProteinExistenceType {
+public class ProteinExistenceType
+{
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the names for the protein and parts thereof.
- * Equivalent to the flat file DE-line.
+ * Describes the names for the protein and parts thereof. Equivalent to the flat
+ * file DE-line.
*
- * <p>Java class for proteinType complex type.
+ * <p>
+ * Java class for proteinType 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="proteinType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "proteinType", propOrder = {
- "recommendedName",
- "alternativeName",
- "submittedName",
- "allergenName",
- "biotechName",
- "cdAntigenName",
- "innName",
- "domain",
- "component"
-})
-public class ProteinType {
+@XmlType(
+ name = "proteinType",
+ propOrder =
+ { "recommendedName", "alternativeName", "submittedName", "allergenName",
+ "biotechName", "cdAntigenName", "innName", "domain", "component" })
+public class ProteinType
+{
+
+ protected ProteinType.RecommendedName recommendedName;
+
+ protected List<ProteinType.AlternativeName> alternativeName;
+
+ protected List<ProteinType.SubmittedName> submittedName;
+
+ protected EvidencedStringType allergenName;
+
+ protected EvidencedStringType biotechName;
+
+ protected List<EvidencedStringType> cdAntigenName;
+
+ protected List<EvidencedStringType> innName;
+
+ protected List<ProteinType.Domain> domain;
+
+ protected List<ProteinType.Component> component;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return possible object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName()
+ {
+ return recommendedName;
+ }
+
+ /**
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value)
+ {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName 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 alternativeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAlternativeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.AlternativeName }
+ *
+ *
+ */
+ public List<ProteinType.AlternativeName> getAlternativeName()
+ {
+ if (alternativeName == null)
+ {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
+ }
+
+ /**
+ * Gets the value of the submittedName 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 submittedName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSubmittedName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.SubmittedName }
+ *
+ *
+ */
+ public List<ProteinType.SubmittedName> getSubmittedName()
+ {
+ if (submittedName == null)
+ {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
+ }
+
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName()
+ {
+ return allergenName;
+ }
+
+ /**
+ * Sets the value of the allergenName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setAllergenName(EvidencedStringType value)
+ {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getBiotechName()
+ {
+ return biotechName;
+ }
+
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value)
+ {
+ this.biotechName = value;
+ }
+
+ /**
+ * Gets the value of the cdAntigenName 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 cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName()
+ {
+ if (cdAntigenName == null)
+ {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
+
+ /**
+ * Gets the value of the innName 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 innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getInnName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getInnName()
+ {
+ if (innName == null)
+ {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
+ /**
+ * Gets the value of the domain 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 domain property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDomain().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.Domain }
+ *
+ *
+ */
+ public List<ProteinType.Domain> getDomain()
+ {
+ if (domain == null)
+ {
+ domain = new ArrayList<ProteinType.Domain>();
+ }
+ return this.domain;
+ }
+
+ /**
+ * Gets the value of the component 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 component property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getComponent().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.Component }
+ *
+ *
+ */
+ public List<ProteinType.Component> getComponent()
+ {
+ if (component == null)
+ {
+ component = new ArrayList<ProteinType.Component>();
+ }
+ return this.component;
+ }
+
+ /**
+ * <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="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+ public static class AlternativeName
+ {
+
+ protected EvidencedStringType fullName;
+
+ protected List<EvidencedStringType> shortName;
+
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName()
+ {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value)
+ {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the shortName 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 shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getShortName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getShortName()
+ {
+ if (shortName == null)
+ {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
+ }
+
+ /**
+ * Gets the value of the ecNumber 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 ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber()
+ {
+ if (ecNumber == null)
+ {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
+ }
+
+ /**
+ * <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">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "recommendedName", "alternativeName", "submittedName", "allergenName",
+ "biotechName", "cdAntigenName", "innName" })
+ public static class Component
+ {
protected ProteinType.RecommendedName recommendedName;
+
protected List<ProteinType.AlternativeName> alternativeName;
+
protected List<ProteinType.SubmittedName> submittedName;
+
protected EvidencedStringType allergenName;
+
protected EvidencedStringType biotechName;
+
protected List<EvidencedStringType> cdAntigenName;
+
protected List<EvidencedStringType> innName;
- protected List<ProteinType.Domain> domain;
- protected List<ProteinType.Component> component;
/**
* Gets the value of the recommendedName property.
*
- * @return
- * possible object is
- * {@link ProteinType.RecommendedName }
- *
+ * @return possible object is {@link ProteinType.RecommendedName }
+ *
*/
- public ProteinType.RecommendedName getRecommendedName() {
- return recommendedName;
+ public ProteinType.RecommendedName getRecommendedName()
+ {
+ return recommendedName;
}
/**
* Sets the value of the recommendedName property.
*
* @param value
- * allowed object is
- * {@link ProteinType.RecommendedName }
- *
+ * allowed object is {@link ProteinType.RecommendedName }
+ *
*/
- public void setRecommendedName(ProteinType.RecommendedName value) {
- this.recommendedName = value;
+ public void setRecommendedName(ProteinType.RecommendedName value)
+ {
+ this.recommendedName = value;
}
/**
* Gets the value of the alternativeName 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 alternativeName property.
+ * 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 alternativeName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getAlternativeName().add(newItem);
+ * getAlternativeName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<ProteinType.AlternativeName> getAlternativeName() {
- if (alternativeName == null) {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
+ public List<ProteinType.AlternativeName> getAlternativeName()
+ {
+ if (alternativeName == null)
+ {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
}
/**
* Gets the value of the submittedName 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 submittedName property.
+ * 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 submittedName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getSubmittedName().add(newItem);
+ * getSubmittedName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<ProteinType.SubmittedName> getSubmittedName() {
- if (submittedName == null) {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
+ public List<ProteinType.SubmittedName> getSubmittedName()
+ {
+ if (submittedName == null)
+ {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
}
/**
* Gets the value of the allergenName property.
*
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
+ * @return possible object is {@link EvidencedStringType }
+ *
*/
- public EvidencedStringType getAllergenName() {
- return allergenName;
+ public EvidencedStringType getAllergenName()
+ {
+ return allergenName;
}
/**
* Sets the value of the allergenName property.
*
* @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
+ * allowed object is {@link EvidencedStringType }
+ *
*/
- public void setAllergenName(EvidencedStringType value) {
- this.allergenName = value;
+ public void setAllergenName(EvidencedStringType value)
+ {
+ this.allergenName = value;
}
/**
* Gets the value of the biotechName property.
*
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
+ * @return possible object is {@link EvidencedStringType }
+ *
*/
- public EvidencedStringType getBiotechName() {
- return biotechName;
+ public EvidencedStringType getBiotechName()
+ {
+ return biotechName;
}
/**
* Sets the value of the biotechName property.
*
* @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
+ * allowed object is {@link EvidencedStringType }
+ *
*/
- public void setBiotechName(EvidencedStringType value) {
- this.biotechName = value;
+ public void setBiotechName(EvidencedStringType value)
+ {
+ this.biotechName = value;
}
/**
* Gets the value of the cdAntigenName 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 cdAntigenName property.
+ * 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 cdAntigenName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getCdAntigenName().add(newItem);
+ * getCdAntigenName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<EvidencedStringType> getCdAntigenName() {
- if (cdAntigenName == null) {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
+ public List<EvidencedStringType> getCdAntigenName()
+ {
+ if (cdAntigenName == null)
+ {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
}
/**
* Gets the value of the innName 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 innName property.
+ * 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 innName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getInnName().add(newItem);
+ * getInnName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<EvidencedStringType> getInnName() {
- if (innName == null) {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
+ public List<EvidencedStringType> getInnName()
+ {
+ if (innName == null)
+ {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
+ }
+
+ /**
+ * <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">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "recommendedName", "alternativeName", "submittedName", "allergenName",
+ "biotechName", "cdAntigenName", "innName" })
+ public static class Domain
+ {
+
+ protected ProteinType.RecommendedName recommendedName;
+
+ protected List<ProteinType.AlternativeName> alternativeName;
+
+ protected List<ProteinType.SubmittedName> submittedName;
+
+ protected EvidencedStringType allergenName;
+
+ protected EvidencedStringType biotechName;
+
+ protected List<EvidencedStringType> cdAntigenName;
+
+ protected List<EvidencedStringType> innName;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return possible object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName()
+ {
+ return recommendedName;
}
/**
- * Gets the value of the domain property.
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value)
+ {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName 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 domain property.
+ * 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 alternativeName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getDomain().add(newItem);
+ * getAlternativeName().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link ProteinType.Domain }
+ * {@link ProteinType.AlternativeName }
*
*
*/
- public List<ProteinType.Domain> getDomain() {
- if (domain == null) {
- domain = new ArrayList<ProteinType.Domain>();
- }
- return this.domain;
+ public List<ProteinType.AlternativeName> getAlternativeName()
+ {
+ if (alternativeName == null)
+ {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
}
/**
- * Gets the value of the component property.
+ * Gets the value of the submittedName 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 component property.
+ * 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 submittedName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getComponent().add(newItem);
+ * getSubmittedName().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link ProteinType.Component }
+ * {@link ProteinType.SubmittedName }
*
*
*/
- public List<ProteinType.Component> getComponent() {
- if (component == null) {
- component = new ArrayList<ProteinType.Component>();
- }
- return this.component;
+ public List<ProteinType.SubmittedName> getSubmittedName()
+ {
+ if (submittedName == null)
+ {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
}
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName()
+ {
+ return allergenName;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the allergenName property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link EvidencedStringType }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
- * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setAllergenName(EvidencedStringType value)
+ {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
*
+ * @return possible object is {@link EvidencedStringType }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "fullName",
- "shortName",
- "ecNumber"
- })
- public static class AlternativeName {
-
- protected EvidencedStringType fullName;
- protected List<EvidencedStringType> shortName;
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName() {
- return fullName;
- }
-
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value) {
- this.fullName = value;
- }
-
- /**
- * Gets the value of the shortName 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 shortName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getShortName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getShortName() {
- if (shortName == null) {
- shortName = new ArrayList<EvidencedStringType>();
- }
- return this.shortName;
- }
-
- /**
- * Gets the value of the ecNumber 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 ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEcNumber().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getEcNumber() {
- if (ecNumber == null) {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
+ public EvidencedStringType getBiotechName()
+ {
+ return biotechName;
+ }
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value)
+ {
+ this.biotechName = value;
}
+ /**
+ * Gets the value of the cdAntigenName 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 cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName()
+ {
+ if (cdAntigenName == null)
+ {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the innName property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getInnName().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "recommendedName",
- "alternativeName",
- "submittedName",
- "allergenName",
- "biotechName",
- "cdAntigenName",
- "innName"
- })
- public static class Component {
-
- protected ProteinType.RecommendedName recommendedName;
- protected List<ProteinType.AlternativeName> alternativeName;
- protected List<ProteinType.SubmittedName> submittedName;
- protected EvidencedStringType allergenName;
- protected EvidencedStringType biotechName;
- protected List<EvidencedStringType> cdAntigenName;
- protected List<EvidencedStringType> innName;
-
- /**
- * Gets the value of the recommendedName property.
- *
- * @return
- * possible object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName getRecommendedName() {
- return recommendedName;
- }
-
- /**
- * Sets the value of the recommendedName property.
- *
- * @param value
- * allowed object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public void setRecommendedName(ProteinType.RecommendedName value) {
- this.recommendedName = value;
- }
-
- /**
- * Gets the value of the alternativeName 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 alternativeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlternativeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.AlternativeName }
- *
- *
- */
- public List<ProteinType.AlternativeName> getAlternativeName() {
- if (alternativeName == null) {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
- }
-
- /**
- * Gets the value of the submittedName 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 submittedName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSubmittedName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.SubmittedName }
- *
- *
- */
- public List<ProteinType.SubmittedName> getSubmittedName() {
- if (submittedName == null) {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
- }
-
- /**
- * Gets the value of the allergenName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getAllergenName() {
- return allergenName;
- }
-
- /**
- * Sets the value of the allergenName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setAllergenName(EvidencedStringType value) {
- this.allergenName = value;
- }
-
- /**
- * Gets the value of the biotechName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getBiotechName() {
- return biotechName;
- }
-
- /**
- * Sets the value of the biotechName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setBiotechName(EvidencedStringType value) {
- this.biotechName = value;
- }
-
- /**
- * Gets the value of the cdAntigenName 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 cdAntigenName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCdAntigenName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getCdAntigenName() {
- if (cdAntigenName == null) {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
- }
-
- /**
- * Gets the value of the innName 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 innName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getInnName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getInnName() {
- if (innName == null) {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
- }
+ public List<EvidencedStringType> getInnName()
+ {
+ if (innName == null)
+ {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+ }
+
+ /**
+ * <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="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+ public static class RecommendedName
+ {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+
+ protected List<EvidencedStringType> shortName;
+
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName()
+ {
+ return fullName;
}
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value)
+ {
+ this.fullName = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the shortName property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getShortName().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "recommendedName",
- "alternativeName",
- "submittedName",
- "allergenName",
- "biotechName",
- "cdAntigenName",
- "innName"
- })
- public static class Domain {
-
- protected ProteinType.RecommendedName recommendedName;
- protected List<ProteinType.AlternativeName> alternativeName;
- protected List<ProteinType.SubmittedName> submittedName;
- protected EvidencedStringType allergenName;
- protected EvidencedStringType biotechName;
- protected List<EvidencedStringType> cdAntigenName;
- protected List<EvidencedStringType> innName;
-
- /**
- * Gets the value of the recommendedName property.
- *
- * @return
- * possible object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName getRecommendedName() {
- return recommendedName;
- }
-
- /**
- * Sets the value of the recommendedName property.
- *
- * @param value
- * allowed object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public void setRecommendedName(ProteinType.RecommendedName value) {
- this.recommendedName = value;
- }
-
- /**
- * Gets the value of the alternativeName 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 alternativeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlternativeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.AlternativeName }
- *
- *
- */
- public List<ProteinType.AlternativeName> getAlternativeName() {
- if (alternativeName == null) {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
- }
-
- /**
- * Gets the value of the submittedName 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 submittedName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSubmittedName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.SubmittedName }
- *
- *
- */
- public List<ProteinType.SubmittedName> getSubmittedName() {
- if (submittedName == null) {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
- }
-
- /**
- * Gets the value of the allergenName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getAllergenName() {
- return allergenName;
- }
-
- /**
- * Sets the value of the allergenName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setAllergenName(EvidencedStringType value) {
- this.allergenName = value;
- }
-
- /**
- * Gets the value of the biotechName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getBiotechName() {
- return biotechName;
- }
-
- /**
- * Sets the value of the biotechName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setBiotechName(EvidencedStringType value) {
- this.biotechName = value;
- }
-
- /**
- * Gets the value of the cdAntigenName 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 cdAntigenName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCdAntigenName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getCdAntigenName() {
- if (cdAntigenName == null) {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
- }
-
- /**
- * Gets the value of the innName 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 innName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getInnName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getInnName() {
- if (innName == null) {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
- }
-
+ public List<EvidencedStringType> getShortName()
+ {
+ if (shortName == null)
+ {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the ecNumber 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 ecNumber property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
- * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getEcNumber().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "fullName",
- "shortName",
- "ecNumber"
- })
- public static class RecommendedName {
-
- @XmlElement(required = true)
- protected EvidencedStringType fullName;
- protected List<EvidencedStringType> shortName;
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName() {
- return fullName;
- }
-
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value) {
- this.fullName = value;
- }
-
- /**
- * Gets the value of the shortName 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 shortName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getShortName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getShortName() {
- if (shortName == null) {
- shortName = new ArrayList<EvidencedStringType>();
- }
- return this.shortName;
- }
-
- /**
- * Gets the value of the ecNumber 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 ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEcNumber().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getEcNumber() {
- if (ecNumber == null) {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
+ public List<EvidencedStringType> getEcNumber()
+ {
+ if (ecNumber == null)
+ {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
+ }
+
+ /**
+ * <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="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "fullName", "ecNumber" })
+ public static class SubmittedName
+ {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+
+ protected List<EvidencedStringType> ecNumber;
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName()
+ {
+ return fullName;
}
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value)
+ {
+ this.fullName = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the ecNumber property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getEcNumber().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "fullName",
- "ecNumber"
- })
- public static class SubmittedName {
-
- @XmlElement(required = true)
- protected EvidencedStringType fullName;
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName() {
- return fullName;
- }
-
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value) {
- this.fullName = value;
- }
-
- /**
- * Gets the value of the ecNumber 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 ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEcNumber().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getEcNumber() {
- if (ecNumber == null) {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
-
+ public List<EvidencedStringType> getEcNumber()
+ {
+ if (ecNumber == null)
+ {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes a chemical reaction.
*
- * <p>Java class for reactionType complex type.
+ * <p>
+ * Java class for reactionType 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="reactionType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "reactionType", propOrder = {
- "text",
- "dbReference"
-})
-public class ReactionType {
+@XmlType(name = "reactionType", propOrder = { "text", "dbReference" })
+public class ReactionType
+{
- @XmlElement(required = true)
- protected String text;
- @XmlElement(required = true)
- protected List<DbReferenceType> dbReference;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected String text;
- /**
- * Gets the value of the text property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getText() {
- return text;
- }
+ @XmlElement(required = true)
+ protected List<DbReferenceType> dbReference;
- /**
- * Sets the value of the text property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setText(String value) {
- this.text = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getText()
+ {
+ return text;
+ }
+
+ /**
+ * Sets the value of the text property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setText(String value)
+ {
+ this.text = value;
+ }
- /**
- * Gets the value of the dbReference 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 dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
+ /**
+ * Gets the value of the dbReference 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 dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
}
+ return this.dbReference;
+ }
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a citation and a summary of its content.
- * Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
+ * Describes a citation and a summary of its content. Equivalent to the flat
+ * file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
*
- * <p>Java class for referenceType complex type.
+ * <p>
+ * Java class for referenceType 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="referenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "referenceType", propOrder = {
- "citation",
- "scope",
- "source"
-})
-public class ReferenceType {
-
- @XmlElement(required = true)
- protected CitationType citation;
- @XmlElement(required = true)
- protected List<String> scope;
- protected SourceDataType source;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "key", required = true)
- protected String key;
-
- /**
- * Gets the value of the citation property.
- *
- * @return
- * possible object is
- * {@link CitationType }
- *
- */
- public CitationType getCitation() {
- return citation;
- }
+@XmlType(
+ name = "referenceType",
+ propOrder =
+ { "citation", "scope", "source" })
+public class ReferenceType
+{
- /**
- * Sets the value of the citation property.
- *
- * @param value
- * allowed object is
- * {@link CitationType }
- *
- */
- public void setCitation(CitationType value) {
- this.citation = value;
- }
+ @XmlElement(required = true)
+ protected CitationType citation;
- /**
- * Gets the value of the scope 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 scope property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getScope().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getScope() {
- if (scope == null) {
- scope = new ArrayList<String>();
- }
- return this.scope;
- }
+ @XmlElement(required = true)
+ protected List<String> scope;
- /**
- * Gets the value of the source property.
- *
- * @return
- * possible object is
- * {@link SourceDataType }
- *
- */
- public SourceDataType getSource() {
- return source;
- }
+ protected SourceDataType source;
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is
- * {@link SourceDataType }
- *
- */
- public void setSource(SourceDataType value) {
- this.source = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+
+ /**
+ * Gets the value of the citation property.
+ *
+ * @return possible object is {@link CitationType }
+ *
+ */
+ public CitationType getCitation()
+ {
+ return citation;
+ }
- /**
- * Gets the value of the key property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey() {
- return key;
+ /**
+ * Sets the value of the citation property.
+ *
+ * @param value
+ * allowed object is {@link CitationType }
+ *
+ */
+ public void setCitation(CitationType value)
+ {
+ this.citation = value;
+ }
+
+ /**
+ * Gets the value of the scope 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 scope property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getScope().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getScope()
+ {
+ if (scope == null)
+ {
+ scope = new ArrayList<String>();
}
+ return this.scope;
+ }
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return possible object is {@link SourceDataType }
+ *
+ */
+ public SourceDataType getSource()
+ {
+ return source;
+ }
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setKey(String value) {
- this.key = value;
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is {@link SourceDataType }
+ *
+ */
+ public void setSource(SourceDataType value)
+ {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the evidence 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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * 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;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlValue;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <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">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sequenceType", propOrder = {
- "value"
-})
-public class SequenceType {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "length", required = true)
- protected int length;
- @XmlAttribute(name = "mass", required = true)
- protected int mass;
- @XmlAttribute(name = "checksum", required = true)
- protected String checksum;
- @XmlAttribute(name = "modified", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar modified;
- @XmlAttribute(name = "version", required = true)
- protected int version;
- @XmlAttribute(name = "precursor")
- protected Boolean precursor;
- @XmlAttribute(name = "fragment")
- protected String fragment;
-
- /**
- * 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 length property.
- *
- */
- public int getLength() {
- return length;
- }
-
- /**
- * Sets the value of the length property.
- *
- */
- public void setLength(int value) {
- this.length = value;
- }
-
- /**
- * Gets the value of the mass property.
- *
- */
- public int getMass() {
- return mass;
- }
-
- /**
- * Sets the value of the mass property.
- *
- */
- public void setMass(int value) {
- this.mass = value;
- }
-
- /**
- * Gets the value of the checksum property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getChecksum() {
- return checksum;
- }
-
- /**
- * Sets the value of the checksum property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setChecksum(String value) {
- this.checksum = value;
- }
-
- /**
- * Gets the value of the modified property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getModified() {
- return modified;
- }
-
- /**
- * Sets the value of the modified property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setModified(XMLGregorianCalendar value) {
- this.modified = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- */
- public int getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- */
- public void setVersion(int value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the precursor property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPrecursor() {
- return precursor;
- }
-
- /**
- * Sets the value of the precursor property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPrecursor(Boolean value) {
- this.precursor = value;
- }
-
- /**
- * Gets the value of the fragment property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFragment() {
- return fragment;
- }
-
- /**
- * Sets the value of the fragment property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFragment(String value) {
- this.fragment = value;
- }
+@XmlType(name = "sequenceType", propOrder = { "value" })
+public class SequenceType
+{
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "length", required = true)
+ protected int length;
+
+ @XmlAttribute(name = "mass", required = true)
+ protected int mass;
+
+ @XmlAttribute(name = "checksum", required = true)
+ protected String checksum;
+
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
+
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
+
+ @XmlAttribute(name = "precursor")
+ protected Boolean precursor;
+
+ @XmlAttribute(name = "fragment")
+ protected String fragment;
+
+ /**
+ * 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 length property.
+ *
+ */
+ public int getLength()
+ {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ */
+ public void setLength(int value)
+ {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the mass property.
+ *
+ */
+ public int getMass()
+ {
+ return mass;
+ }
+
+ /**
+ * Sets the value of the mass property.
+ *
+ */
+ public void setMass(int value)
+ {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the checksum property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getChecksum()
+ {
+ return checksum;
+ }
+
+ /**
+ * Sets the value of the checksum property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setChecksum(String value)
+ {
+ this.checksum = value;
+ }
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified()
+ {
+ return modified;
+ }
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value)
+ {
+ this.modified = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the precursor property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPrecursor()
+ {
+ return precursor;
+ }
+
+ /**
+ * Sets the value of the precursor property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPrecursor(Boolean value)
+ {
+ this.precursor = value;
+ }
+
+ /**
+ * Gets the value of the fragment property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFragment()
+ {
+ return fragment;
+ }
+
+ /**
+ * Sets the value of the fragment property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFragment(String value)
+ {
+ this.fragment = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * Describes the source of the sequence according to the citation.
- * Equivalent to the flat file RC-line.
+ * Describes the source of the sequence according to the citation. Equivalent to
+ * the flat file RC-line.
*
- * <p>Java class for sourceDataType complex type.
+ * <p>
+ * Java class for sourceDataType 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="sourceDataType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceDataType", propOrder = {
- "strainOrPlasmidOrTransposon"
-})
-public class SourceDataType {
-
- @XmlElements({
- @XmlElement(name = "strain", type = SourceDataType.Strain.class),
- @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
- @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
- @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
- })
- protected List<Object> strainOrPlasmidOrTransposon;
+@XmlType(
+ name = "sourceDataType",
+ propOrder =
+ { "strainOrPlasmidOrTransposon" })
+public class SourceDataType
+{
+
+ @XmlElements({
+ @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+ @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+ @XmlElement(
+ name = "transposon",
+ type = SourceDataType.Transposon.class),
+ @XmlElement(name = "tissue", type = SourceDataType.Tissue.class) })
+ protected List<Object> strainOrPlasmidOrTransposon;
+
+ /**
+ * Gets the value of the strainOrPlasmidOrTransposon 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 strainOrPlasmidOrTransposon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getStrainOrPlasmidOrTransposon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SourceDataType.Strain } {@link SourceDataType.Plasmid }
+ * {@link SourceDataType.Transposon } {@link SourceDataType.Tissue }
+ *
+ *
+ */
+ public List<Object> getStrainOrPlasmidOrTransposon()
+ {
+ if (strainOrPlasmidOrTransposon == null)
+ {
+ strainOrPlasmidOrTransposon = new ArrayList<Object>();
+ }
+ return this.strainOrPlasmidOrTransposon;
+ }
+
+ /**
+ * <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">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Plasmid
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
/**
- * Gets the value of the strainOrPlasmidOrTransposon property.
+ * 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 evidence 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 strainOrPlasmidOrTransposon property.
+ * 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 evidence property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getStrainOrPlasmidOrTransposon().add(newItem);
+ * getEvidence().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SourceDataType.Strain }
- * {@link SourceDataType.Plasmid }
- * {@link SourceDataType.Transposon }
- * {@link SourceDataType.Tissue }
+ * Objects of the following type(s) are allowed in the list {@link Integer }
*
*
*/
- public List<Object> getStrainOrPlasmidOrTransposon() {
- if (strainOrPlasmidOrTransposon == null) {
- strainOrPlasmidOrTransposon = new ArrayList<Object>();
- }
- return this.strainOrPlasmidOrTransposon;
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
+ }
+
+ /**
+ * <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">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Strain
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the value property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
+ */
+ public String getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Plasmid {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the evidence property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
+ * getEvidence().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Strain {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ }
+
+ /**
+ * <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">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Tissue
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ /**
+ * 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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the evidence property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
+ * getEvidence().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Tissue {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+ }
+
+ /**
+ * <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">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Transposon
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * 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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the evidence property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <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 evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
+ * getEvidence().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Transposon {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * 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 evidence 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 evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
-
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
+ }
+
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
+ * Describes the source of the data using a database cross-reference (or a 'ref'
+ * attribute when the source cannot be found in a public data source, such as
+ * PubMed, and is cited only within the UniProtKB entry).
*
- * <p>Java class for sourceType complex type.
+ * <p>
+ * Java class for sourceType 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="sourceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceType", propOrder = {
- "dbReference"
-})
-public class SourceType {
+@XmlType(name = "sourceType", propOrder = { "dbReference" })
+public class SourceType
+{
+
+ protected DbReferenceType dbReference;
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "ref")
- protected BigInteger ref;
+ @XmlAttribute(name = "ref")
+ protected BigInteger ref;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
- /**
- * Gets the value of the ref property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getRef() {
- return ref;
- }
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getRef()
+ {
+ return ref;
+ }
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setRef(BigInteger value) {
- this.ref = value;
- }
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setRef(BigInteger value)
+ {
+ this.ref = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Indicates whether the name of a plasmid is known or unknown.
*
- * <p>Java class for statusType complex type.
+ * <p>
+ * Java class for statusType 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="statusType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "statusType", propOrder = {
- "value"
-})
-public class StatusType {
+@XmlType(name = "statusType", propOrder = { "value" })
+public class StatusType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "status")
- protected String status;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * 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 value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- if (status == null) {
- return "known";
- } else {
- return status;
- }
- }
+ /**
+ * 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 status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
+ /**
+ * Gets the value of the status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ if (status == null)
+ {
+ return "known";
+ }
+ else
+ {
+ return status;
}
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStatus(String value)
+ {
+ this.status = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the subcellular location and optionally the topology and orientation of a molecule.
+ * Describes the subcellular location and optionally the topology and
+ * orientation of a molecule.
*
- * <p>Java class for subcellularLocationType complex type.
+ * <p>
+ * Java class for subcellularLocationType 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="subcellularLocationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "subcellularLocationType", propOrder = {
- "location",
- "topology",
- "orientation"
-})
-public class SubcellularLocationType {
+@XmlType(
+ name = "subcellularLocationType",
+ propOrder =
+ { "location", "topology", "orientation" })
+public class SubcellularLocationType
+{
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> location;
+
+ protected List<EvidencedStringType> topology;
- @XmlElement(required = true)
- protected List<EvidencedStringType> location;
- protected List<EvidencedStringType> topology;
- protected List<EvidencedStringType> orientation;
+ protected List<EvidencedStringType> orientation;
- /**
- * Gets the value of the location 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 location property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getLocation() {
- if (location == null) {
- location = new ArrayList<EvidencedStringType>();
- }
- return this.location;
+ /**
+ * Gets the value of the location 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 location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getLocation()
+ {
+ if (location == null)
+ {
+ location = new ArrayList<EvidencedStringType>();
}
+ return this.location;
+ }
- /**
- * Gets the value of the topology 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 topology property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTopology().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getTopology() {
- if (topology == null) {
- topology = new ArrayList<EvidencedStringType>();
- }
- return this.topology;
+ /**
+ * Gets the value of the topology 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 topology property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getTopology().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getTopology()
+ {
+ if (topology == null)
+ {
+ topology = new ArrayList<EvidencedStringType>();
}
+ return this.topology;
+ }
- /**
- * Gets the value of the orientation 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 orientation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getOrientation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getOrientation() {
- if (orientation == null) {
- orientation = new ArrayList<EvidencedStringType>();
- }
- return this.orientation;
+ /**
+ * Gets the value of the orientation 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 orientation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getOrientation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getOrientation()
+ {
+ if (orientation == null)
+ {
+ orientation = new ArrayList<EvidencedStringType>();
}
+ return this.orientation;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-
package jalview.xml.binding.uniprot;
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>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "entry",
- "copyright"
-})
+@XmlType(name = "", propOrder = { "entry", "copyright" })
@XmlRootElement(name = "uniprot")
-public class Uniprot {
+public class Uniprot
+{
- @XmlElement(required = true)
- protected List<Entry> entry;
- protected String copyright;
+ @XmlElement(required = true)
+ protected List<Entry> entry;
- /**
- * Gets the value of the entry 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 entry property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEntry().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry }
- *
- *
- */
- public List<Entry> getEntry() {
- if (entry == null) {
- entry = new ArrayList<Entry>();
- }
- return this.entry;
- }
+ protected String copyright;
- /**
- * Gets the value of the copyright property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCopyright() {
- return copyright;
+ /**
+ * Gets the value of the entry 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 entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Entry }
+ *
+ *
+ */
+ public List<Entry> getEntry()
+ {
+ if (entry == null)
+ {
+ entry = new ArrayList<Entry>();
}
+ return this.entry;
+ }
- /**
- * Sets the value of the copyright property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCopyright(String value) {
- this.copyright = value;
- }
+ /**
+ * Gets the value of the copyright property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCopyright()
+ {
+ return copyright;
+ }
+
+ /**
+ * Sets the value of the copyright property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCopyright(String value)
+ {
+ this.copyright = value;
+ }
}
// Generated on: 2023.05.13 at 06:58:42 PM BST
//
-@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+ namespace = "http://uniprot.org/uniprot",
+ elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.uniprot;
dsq.addAlignmentAnnotation(ana);
if (cm != null && cm instanceof MappableContactMatrixI)
{
- dsq.addContactListFor(ana, ((MappableContactMatrixI) cm).liftOver(dsq,sqmpping));
+ dsq.addContactListFor(ana, ((MappableContactMatrixI) cm)
+ .liftOver(dsq, sqmpping));
}
}
else
// Useful for debugging mappings - adds annotation for mapped position
float min = -1, max = 0;
Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
- for (int i = sq.getStart(), j = sq.getEnd(),
- k = 0; i <= j; i++, k++)
+ for (int i = sq.getStart(), j = sq
+ .getEnd(), k = 0; i <= j; i++, k++)
{
int prn = mapping.getPDBResNum(k + 1);
assertSame(seq, cds1.getDatasetSequence());
}
-
@Test(groups = "Functional")
public void testAddReferenceAnnotations()
{
- SequenceI longseq= new Sequence("longA","ASDASDASDASDAASDASDASDASDA");
+ SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
Annotation[] aa = new Annotation[longseq.getLength()];
-
- for (int p=0;p<aa.length; p++)
+
+ for (int p = 0; p < aa.length; p++)
{
- aa[p] = new Annotation("P", "pos "+(p+1), (char)0, (float)p+1);
+ aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0,
+ (float) p + 1);
}
- AlignmentAnnotation refAnnot=new AlignmentAnnotation("LongSeqAnnot","Annotations",aa);
+ AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot",
+ "Annotations", aa);
refAnnot.setCalcId("Test");
longseq.addAlignmentAnnotation(refAnnot);
verifyExpectedSequenceAnnotation(refAnnot);
- Alignment ourAl = new Alignment(new SequenceI[] { longseq.getSubSequence(5, 10),longseq.getSubSequence(7, 12)});
+ Alignment ourAl = new Alignment(
+ new SequenceI[]
+ { longseq.getSubSequence(5, 10),
+ longseq.getSubSequence(7, 12) });
ourAl.createDatasetAlignment();
-
+
// transfer annotation
SortedMap<String, String> tipEntries = new TreeMap<>();
Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
assertNotNull(ourAl.getAlignmentAnnotation());
- assertEquals(ourAl.getAlignmentAnnotation().length,2);
-
- for (AlignmentAnnotation alan:ourAl.getAlignmentAnnotation())
+ assertEquals(ourAl.getAlignmentAnnotation().length, 2);
+
+ for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
{
verifyExpectedSequenceAnnotation(alan);
}
// now simulate copy/paste to new alignment
SequenceI[] newSeqAl = new SequenceI[2];
// copy sequences but no annotation
- newSeqAl[0]=new Sequence(ourAl.getSequenceAt(0),ourAl.getSequenceAt(0).getAnnotation());
- newSeqAl[1]=new Sequence(ourAl.getSequenceAt(1),ourAl.getSequenceAt(1).getAnnotation());
-
+ newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
+ ourAl.getSequenceAt(0).getAnnotation());
+ newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
+ ourAl.getSequenceAt(1).getAnnotation());
+
Alignment newAl = new Alignment(newSeqAl);
// delete annotation
- for (SequenceI sq:newAl.getSequences())
+ for (SequenceI sq : newAl.getSequences())
{
sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
}
SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
sg.setStartRes(0);
sg.setEndRes(newAl.getWidth());
- AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0], newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
- AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1], newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
- for (AlignmentAnnotation alan:newAl.getAlignmentAnnotation())
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
+ newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
+ newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+ for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
{
verifyExpectedSequenceAnnotation(alan);
}
}
-
+
/**
- * helper - tests annotation is mapped to position it was originally created for
+ * helper - tests annotation is mapped to position it was originally created
+ * for
+ *
* @param alan
*/
private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
{
- for (int c=0;c<alan.annotations.length;c++)
+ for (int c = 0; c < alan.annotations.length; c++)
{
Annotation a = alan.annotations[c];
- if (a!=null)
+ if (a != null)
{
- assertEquals("Misaligned annotation at "+c,(float)alan.sequenceRef.findPosition(c),a.value);
- } else {
- assertTrue("Unexpected Null at position "+c,c>=alan.sequenceRef.getLength() || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
+ assertEquals("Misaligned annotation at " + c,
+ (float) alan.sequenceRef.findPosition(c), a.value);
+ }
+ else
+ {
+ assertTrue("Unexpected Null at position " + c,
+ c >= alan.sequenceRef.getLength()
+ || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
}
}
}
AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
.iterator().next();
ContactMatrixI t_cm = al.getContactMatrixFor(alan);
- assertNotNull("No contact map for the transferred annotation row.",t_cm);
+ assertNotNull("No contact map for the transferred annotation row.",
+ t_cm);
assertTrue(t_cm instanceof SeqDistanceContactMatrix);
- assertTrue(((SeqDistanceContactMatrix)t_cm).hasReferenceSeq());
-
+ assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
+
ContactListI cl = al.getContactListFor(alan, 1);
assertNotNull(
"No contact matrix recovered after reference annotation transfer",
cl);
- // semantics of sequence associated contact list is slightly tricky - column 3 in alignment should have data
+ // semantics of sequence associated contact list is slightly tricky - column
+ // 3 in alignment should have data
cl = al.getContactListFor(alan, 3);
assertNotNull(
"Contact matrix should have data for last position in sequence",
public class AverageDistanceEngineTest
{
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeMethod(alwaysRun = true)
+ public void loadProperties()
+ {
+ Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testUPGMAEngine() throws Exception
+ {
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/test_fab41.result/sample.a3m", DataSourceType.FILE);
+ AlignmentI seqs = af.getViewport().getAlignment();
+ SequenceI target = seqs.getSequenceAt(0);
+ File testPAE = new File(
+ "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
+ List<Object> pae_obj = (List<Object>) Platform
+ .parseJSON(new FileInputStream(testPAE));
+ if (pae_obj == null)
{
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ Assert.fail("JSON PAE file did not parse properly.");
}
+ ContactMatrixI matrix = new PAEContactMatrix(target,
+ (Map<String, Object>) pae_obj.get(0));
+ AlignmentAnnotation aa = target.addContactList(matrix);
+ System.out.println("Matrix has max=" + matrix.getMax() + " and min="
+ + matrix.getMin());
+ long start = System.currentTimeMillis();
+ AverageDistanceEngine clusterer = new AverageDistanceEngine(
+ af.getViewport(), null, matrix);
+ System.out.println("built a tree in "
+ + (System.currentTimeMillis() - start) * 0.001 + " seconds.");
+ StringBuffer sb = new StringBuffer();
+ System.out.println("Newick string\n"
+ + new jalview.io.NewickFile(clusterer.getTopNode(), true, true)
+ .print());
- @BeforeMethod(alwaysRun = true)
- public void loadProperties()
+ double height = clusterer.findHeight(clusterer.getTopNode());
+ // compute height fraction to cut
+ // PAE matrixes are absolute measure in angstrom, so
+ // cluster all regions within threshold (e.g. 2A) - if height above
+ // threshold. Otherwise all nodes are in one cluster
+ double thr = .2;
+ List<BinaryNode> groups;
+ if (height > thr)
{
- Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
+ float cut = (float) (thr / height);
+ System.out.println("Threshold " + cut + " for height=" + height);
+ groups = clusterer.groupNodes(cut);
}
- @Test(groups={"Functional"})
- public void testUPGMAEngine() throws Exception
+ else
{
- AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded("examples/test_fab41.result/sample.a3m",DataSourceType.FILE);
- AlignmentI seqs = af.getViewport().getAlignment();
- SequenceI target = seqs.getSequenceAt(0);
- File testPAE = new File("examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
- List<Object> pae_obj = (List<Object>) Platform.parseJSON(new FileInputStream(testPAE));
- if (pae_obj == null)
- {
- Assert.fail("JSON PAE file did not parse properly.");
- }
- ContactMatrixI matrix = new PAEContactMatrix(target,
- (Map<String, Object>) pae_obj.get(0));
- AlignmentAnnotation aa = target.addContactList(matrix);
- System.out.println("Matrix has max="+matrix.getMax()+" and min="+matrix.getMin());
- long start = System.currentTimeMillis();
- AverageDistanceEngine clusterer = new AverageDistanceEngine(af.getViewport(), null, matrix);
- System.out.println("built a tree in "+(System.currentTimeMillis()-start)*0.001+" seconds.");
- StringBuffer sb = new StringBuffer();
- System.out.println("Newick string\n"+ new jalview.io.NewickFile(clusterer.getTopNode(),true,true).print());
-
- double height = clusterer.findHeight(clusterer.getTopNode());
- // compute height fraction to cut
- // PAE matrixes are absolute measure in angstrom, so
- // cluster all regions within threshold (e.g. 2A) - if height above threshold. Otherwise all nodes are in one cluster
- double thr=.2;
- List<BinaryNode> groups;
- if (height>thr)
- {
- float cut = (float) (thr/height);
- System.out.println("Threshold "+cut+" for height="+height);
- groups = clusterer.groupNodes(cut);
- } else{
- groups=new ArrayList<BinaryNode>();
- groups.add(clusterer.getTopNode());
- }
- int n=1;
- for (BinaryNode root:groups)
+ groups = new ArrayList<BinaryNode>();
+ groups.add(clusterer.getTopNode());
+ }
+ int n = 1;
+ for (BinaryNode root : groups)
+ {
+ System.out.println("Cluster " + n++);
+ for (BinaryNode leaf : clusterer.findLeaves(root))
{
- System.out.println("Cluster "+n++);
- for (BinaryNode leaf:clusterer.findLeaves(root))
- {
- System.out.print(" "+leaf.getName());
- }
- System.out.println("\\");
+ System.out.print(" " + leaf.getName());
}
-
+ System.out.println("\\");
}
+ }
+
}
// ?
}
- @Test(groups = {"Functional"})
+
+ @Test(groups = { "Functional" })
public void testEquals()
{
SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
SequenceI seq3 = new Sequence("seq2", "-PQR");
AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
a.setDataset(null);
- assertEquals(a.getDataset(),a.getDataset());
+ assertEquals(a.getDataset(), a.getDataset());
}
}
import org.testng.Assert;
import org.testng.annotations.Test;
-public class ContactRangeTest {
+public class ContactRangeTest
+{
@Test
public void testContactRangeBean()
{
ContactRange cr = new ContactRange();
- cr.update(5, 15, 6, 0.2, 12, 1.5,3.7);
+ cr.update(5, 15, 6, 0.2, 12, 1.5, 3.7);
Assert.assertEquals(5, cr.getFrom_column());
Assert.assertEquals(15, cr.getTo_column());
Assert.assertEquals(6, cr.getMinPos());
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- static float[][] PAEdata = {
- {1.0f,2.0f,3.0f,4.0f,5.0f},
- {2.0f,1.0f,2.0f,3.0f,4.0f},
- {3.0f,2.0f,1.0f,2.0f,3.0f},
- {4.0f,3.0f,2.0f,1.0f,2.0f},
- {5.0f,4.0f,3.0f,2.0f,1.0f}};
-
+ static float[][] PAEdata = { { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f },
+ { 2.0f, 1.0f, 2.0f, 3.0f, 4.0f },
+ { 3.0f, 2.0f, 1.0f, 2.0f, 3.0f },
+ { 4.0f, 3.0f, 2.0f, 1.0f, 2.0f },
+ { 5.0f, 4.0f, 3.0f, 2.0f, 1.0f } };
+
/**
* test associations for a PAE matrix
*/
@Test(groups = { "Functional" })
public void testSeqAssociatedPAEMatrix()
{
- Sequence seq = new Sequence("Seq","ASDQE");
- AlignmentAnnotation aa = seq.addContactList(new PAEContactMatrix(seq, PAEdata));
+ Sequence seq = new Sequence("Seq", "ASDQE");
+ AlignmentAnnotation aa = seq
+ .addContactList(new PAEContactMatrix(seq, PAEdata));
assertNotNull(seq.getContactListFor(aa, 0));
- assertEquals(seq.getContactListFor(aa, 0).getContactAt(0),1.0);
+ assertEquals(seq.getContactListFor(aa, 0).getContactAt(0), 1.0);
assertNotNull(seq.getContactListFor(aa, 1));
- assertEquals(seq.getContactListFor(aa, 1).getContactAt(1),1.0);
+ assertEquals(seq.getContactListFor(aa, 1).getContactAt(1), 1.0);
assertNotNull(seq.getContactListFor(aa, 2));
- assertEquals(seq.getContactListFor(aa, 2).getContactAt(2),1.0);
+ assertEquals(seq.getContactListFor(aa, 2).getContactAt(2), 1.0);
assertNotNull(seq.getContactListFor(aa, 3));
- assertEquals(seq.getContactListFor(aa, 3).getContactAt(3),1.0);
+ assertEquals(seq.getContactListFor(aa, 3).getContactAt(3), 1.0);
assertNotNull(seq.getContactListFor(aa, 4));
- assertEquals(seq.getContactListFor(aa, 4).getContactAt(4),1.0);
-
- assertNotNull(seq.getContactListFor(aa, seq.getEnd()-1));
+ assertEquals(seq.getContactListFor(aa, 4).getContactAt(4), 1.0);
+
+ assertNotNull(seq.getContactListFor(aa, seq.getEnd() - 1));
assertNull(seq.getContactListFor(aa, seq.getEnd()));
-
+
ContactListI cm = seq.getContactListFor(aa, seq.getStart());
- assertEquals(cm.getContactAt(seq.getStart()),1d);
- verifyPAEmatrix(seq, aa, 0,0,4);
-
-
+ assertEquals(cm.getContactAt(seq.getStart()), 1d);
+ verifyPAEmatrix(seq, aa, 0, 0, 4);
+
// Now associated with sequence not starting at 1
- seq = new Sequence("Seq/5-9","ASDQE");
+ seq = new Sequence("Seq/5-9", "ASDQE");
ContactMatrixI paematrix = new PAEContactMatrix(seq, PAEdata);
aa = seq.addContactList(paematrix);
assertNotNull(aa);
- // individual annotation elements need to be distinct for Matrix associated rows
- Annotation ae5=aa.getAnnotationForPosition(5);
- Annotation ae6=aa.getAnnotationForPosition(6);
+ // individual annotation elements need to be distinct for Matrix associated
+ // rows
+ Annotation ae5 = aa.getAnnotationForPosition(5);
+ Annotation ae6 = aa.getAnnotationForPosition(6);
assertNotNull(ae5);
assertNotNull(ae6);
- assertTrue(ae5!=ae6);
-
+ assertTrue(ae5 != ae6);
+
cm = seq.getContactListFor(aa, 0);
- assertEquals(cm.getContactAt(0),1d);
+ assertEquals(cm.getContactAt(0), 1d);
verifyPAEmatrix(seq, aa, 0, 0, 4);
// test clustering
paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
-
+
// remap - test the MappableContactMatrix.liftOver method
- SequenceI newseq = new Sequence("Seq","ASDQEASDQEASDQE");
- Mapping sqmap = new Mapping(seq, new MapList(new int[] {5,8,10,10},new int[] { 5,9}, 1, 1));
+ SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+ Mapping sqmap = new Mapping(seq,
+ new MapList(new int[]
+ { 5, 8, 10, 10 }, new int[] { 5, 9 }, 1, 1));
assertTrue(paematrix instanceof MappableContactMatrixI);
-
- MappableContactMatrixI remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
+
+ MappableContactMatrixI remapped = ((MappableContactMatrixI) paematrix)
+ .liftOver(newseq, sqmap);
assertTrue(remapped instanceof PAEContactMatrix);
-
+
AlignmentAnnotation newaa = newseq.addContactList(remapped);
- assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(1)));
- assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(4)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(5)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(6)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(7)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(8)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
// no mapping for position 9
- assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(9)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
// last column
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
// verify MappedPositions includes discontinuity
- int[] mappedCl = newseq.getContactListFor(newaa, 5).getMappedPositionsFor(0, 4);
- assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
-
- // make it harder.
-
+ int[] mappedCl = newseq.getContactListFor(newaa, 5)
+ .getMappedPositionsFor(0, 4);
+ assertEquals(4, mappedCl.length,
+ "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
+ // make it harder.
+
SequenceI alseq = newseq.getSubSequence(6, 10);
alseq.insertCharAt(2, 2, '-');
- AlignmentI alForSeq=new Alignment(new SequenceI[] { alseq });
- newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa, null);
+ AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
+ newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
+ null);
ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
assertNotNull(alcl);
mappedCl = alcl.getMappedPositionsFor(0, 4);
assertNotNull(mappedCl);
- assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
-
+ assertEquals(4, mappedCl.length,
+ "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
// remap2 - test with original matrix map from 1-5 remapped to 5-9
-
- seq = new Sequence("Seq/1-5","ASDQE");
+
+ seq = new Sequence("Seq/1-5", "ASDQE");
paematrix = new PAEContactMatrix(seq, PAEdata);
assertTrue(paematrix instanceof MappableContactMatrixI);
aa = seq.addContactList(paematrix);
-
- newseq = new Sequence("Seq","ASDQEASDQEASDQE");
- sqmap = new Mapping(seq, new MapList(new int[] {5,9},new int[] { 1,5}, 1, 1));
-
- remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
+
+ newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+ sqmap = new Mapping(seq,
+ new MapList(new int[]
+ { 5, 9 }, new int[] { 1, 5 }, 1, 1));
+
+ remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
assertTrue(remapped instanceof PAEContactMatrix);
-
-
+
newaa = newseq.addContactList(remapped);
verify_mapping(newseq, newaa);
// remap3 - remap2 but mapping sense in liftover is reversed
-
- seq = new Sequence("Seq/1-5","ASDQE");
+
+ seq = new Sequence("Seq/1-5", "ASDQE");
paematrix = new PAEContactMatrix(seq, PAEdata);
assertTrue(paematrix instanceof MappableContactMatrixI);
aa = seq.addContactList(paematrix);
-
- newseq = new Sequence("Seq","ASDQEASDQEASDQE");
- sqmap = new Mapping(newseq, new MapList(new int[] { 1,5},new int[] {5,9},1, 1));
-
- remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
+
+ newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+ sqmap = new Mapping(newseq,
+ new MapList(new int[]
+ { 1, 5 }, new int[] { 5, 9 }, 1, 1));
+
+ remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
assertTrue(remapped instanceof PAEContactMatrix);
-
-
+
newaa = newseq.addContactList(remapped);
verify_mapping(newseq, newaa);
}
+
/**
- * checks that the PAE matrix is located at positions 1-9 in newseq, and columns are not truncated.
+ * checks that the PAE matrix is located at positions 1-9 in newseq, and
+ * columns are not truncated.
+ *
* @param newseq
* @param newaa
*/
private void verify_mapping(SequenceI newseq, AlignmentAnnotation newaa)
{
- assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(1)));
- assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(4)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(5)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(6)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(7)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(8)));
- assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(9)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
// last column should be null this time
- assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
-
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
+
verifyPAEmatrix(newseq, newaa, 4, 4, 8);
}
- private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa, int topl, int rowl, int rowr)
+ private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa,
+ int topl, int rowl, int rowr)
{
int[] mappedCl;
- for (int f=rowl;f<=rowr;f++) {
+ for (int f = rowl; f <= rowr; f++)
+ {
ContactListI clist = seq.getContactListFor(aa, f);
- assertNotNull(clist,"No ContactListI for position "+(f));
- assertEquals(clist.getContactAt(0), (double) f-topl+1,"for column "+f+" relative to "+topl);
+ assertNotNull(clist, "No ContactListI for position " + (f));
+ assertEquals(clist.getContactAt(0), (double) f - topl + 1,
+ "for column " + f + " relative to " + topl);
mappedCl = clist.getMappedPositionsFor(0, 0);
assertNotNull(mappedCl);
- assertEquals(mappedCl[0],mappedCl[1]);
- assertEquals(mappedCl[0],seq.findIndex(seq.getStart()+topl));
- assertEquals(clist.getContactAt(f-topl),1d, "for column and row "+f+" relative to "+topl);
- }
+ assertEquals(mappedCl[0], mappedCl[1]);
+ assertEquals(mappedCl[0], seq.findIndex(seq.getStart() + topl));
+ assertEquals(clist.getContactAt(f - topl), 1d,
+ "for column and row " + f + " relative to " + topl);
+ }
}
}
Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
}
-
+
@Test(groups = "Functional")
public void testSetOverviewTitle()
{
OverviewPanel ov1 = this.af.openOverviewPanel(true);
String alignFrameTitle = af.getTitle();
assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
-
+
/*
* on New View, existing overview should get " Original" added to title
* and new view's overview should get " View 1" added
*/
af.newView_actionPerformed(null);
- assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+ assertEquals(ov1.getTitle(),
+ "Overview " + alignFrameTitle + " Original");
OverviewPanel ov2 = this.af.openOverviewPanel(true);
assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
}
-
+
@Test(groups = "Functional")
public void testSetOverviewTitle_automaticOverview()
{
- Cache.setProperty("SHOW_OVERVIEW", "true");
+ Cache.setProperty("SHOW_OVERVIEW", "true");
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel();
assertNotNull(ov1);
String alignFrameTitle = alignFrame.getTitle();
assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
-
+
/*
* on New View, existing overview should get " Original" added to title
* and new view's automatic overview should have " View 1" added
*/
alignFrame.newView_actionPerformed(null);
- assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+ assertEquals(ov1.getTitle(),
+ "Overview " + alignFrameTitle + " Original");
OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel();
assertNotNull(ov2);
assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
}
assertEquals(dna.length(), 51200);
AlignFrame alignFrame = new FileLoader()
- .LoadFileWaitTillLoaded("dna "+dna, DataSourceType.PASTE);
+ .LoadFileWaitTillLoaded("dna " + dna, DataSourceType.PASTE);
SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
AlignViewport av = alignFrame.getViewport();
av.setScaleAboveWrapped(true);
}
@SuppressWarnings("deprecation")
- @Test(groups =
- { "Functional" })
+ @Test(groups = { "Functional" })
public void buildPDBQueryTest()
{
System.out.println("seq >>>> " + seq);
}
@SuppressWarnings("deprecation")
- @Test(groups =
- { "Functional" })
+ @Test(groups = { "Functional" })
public void buildThreeDBQueryTest()
{
System.out.println("seq >>>> " + upSeq);
boolean diffseqcols = false, diffgseqcols = false;
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
assertTrue(__rcs.isSeqAssociated(),
"Group Annotation colourscheme wasn't sequence associated");
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
}
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]);
- dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat,0.5f, false));
+ 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]);
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
// verify store/restore of group bitsets
- for (BitSet gp:dummyMat.getGroups())
+ for (BitSet gp : dummyMat.getGroups())
{
StringBuilder sb = new StringBuilder();
- for (long val:gp.toLongArray())
+ for (long val : gp.toLongArray())
{
- if (sb.length()>0) {
+ if (sb.length() > 0)
+ {
sb.append(",");
}
sb.append(val);
}
String[] longvals = sb.toString().split(",");
long[] newlongvals = new long[longvals.length];
- for (int lv=0;lv<longvals.length;lv++)
+ for (int lv = 0; lv < longvals.length; lv++)
{
- try {
- newlongvals[lv]=Long.valueOf(longvals[lv]);
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
} catch (Exception x)
{
Assert.fail("failed to deserialise bitset element ");
BitSet newGp = BitSet.valueOf(newlongvals);
assertTrue(gp.equals(newGp));
}
-
+
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
".jvp");
new Jalview2XML(false).saveState(tfile);
.getContactMatrixFor(newSeq.getAnnotation()[0]);
Assert.assertNotNull(restoredMat);
MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq);
- MapList newMap = ((MappableContactMatrixI) restoredMat).getMapFor(newSeq);
- Assert.assertEquals(oldMap.getFromRanges(),newMap.getFromRanges());
- Assert.assertEquals(oldMap.getToRanges(),newMap.getToRanges());
- Assert.assertEquals(oldMap.getFromRatio(),newMap.getFromRatio());
- Assert.assertEquals(oldMap.getToRatio(),newMap.getToRatio());
-
+ MapList newMap = ((MappableContactMatrixI) restoredMat)
+ .getMapFor(newSeq);
+ Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges());
+ Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges());
+ Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio());
+ Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio());
+
for (i = sq.getLength() - 1; i >= 0; i--)
{
ContactListI oldCM = dummyMat.getContactList(i),
newCM = restoredMat.getContactList(i);
for (int j = oldCM.getContactHeight(); j >= 0; j--)
{
- double old_j=oldCM.getContactAt(j);
- double new_j=newCM.getContactAt(j);
- Assert.assertEquals(old_j,new_j);
+ double old_j = oldCM.getContactAt(j);
+ double new_j = newCM.getContactAt(j);
+ Assert.assertEquals(old_j, new_j);
}
}
Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
- Assert.assertEquals( restoredMat.getNewick(),dummyMat.getNewick());
-
-
+ Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
}
}
public void testGetColumnColourFromSequence()
{
// gapColour, residueColour, hiddenColour
- OverviewResColourFinder cf = new OverviewResColourFinder(
- Color.PINK, Color.white, Color.green);
+ OverviewResColourFinder cf = new OverviewResColourFinder(Color.PINK,
+ Color.white, Color.green);
Sequence seq1 = new Sequence("seq1", "PQ-RL-");
Sequence seq2 = new Sequence("seq2", "FVE");
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
av.getResidueShading(), groups, seq, 2, null));
// use legacy colouring
- rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+ Color.red);
// G in group specified as magenta in Zappo
assertEquals(Color.magenta, rcf.getResidueColour(false,
assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
// legacy colouring set explicitly via constructor
- rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+ Color.red);
shader = new ResidueShader();
// residues light gray
assertEquals(Color.blue, c);
// legacy colouring with colour scheme
- rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+ Color.red);
// M residue pink
c = rcf.getBoxColour(shader, seq, 0);
@Test(groups = "Functional")
public void testFindFeatureColour_nestedFeatures()
{
- SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120, 0f, null);
+ SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120,
+ 0f, null);
seq.addSequenceFeature(sf1);
SequenceFeature sf2 = new SequenceFeature("domain", "binding", 10, 20,
0f, null);
git://source.jalview.org / jalview.git / commitdiff