}
// ignore case differences
- if (allowmismatch || (c1 == c2) || (Math.abs(c2-c1)==('a'-'A')))
+ if (allowmismatch || (c1 == c2) || (Math.abs(c2 - c1) == ('a' - 'A')))
{
// extend mapping interval
if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
bestm = msq;
}
}
- // jalview.bin.Console.outPrintln("Best Score for " + (matches.size() + 1) + " :"
+ // jalview.bin.Console.outPrintln("Best Score for " + (matches.size() +
+ // 1) + " :"
// + bestscore);
matches.add(bestm);
aligns.add(bestaseq);
if (tmp.size() != nSeq)
{
- jalview.bin.Console.errPrintln("WARNING: tmp.size()=" + tmp.size() + " != nseq="
- + nSeq
+ jalview.bin.Console.errPrintln("WARNING: tmp.size()=" + tmp.size()
+ + " != nseq=" + nSeq
+ " in getOrderByTree - tree contains sequences not in alignment");
}
}
int featureCount = feats[i] == null ? 0
: ((SequenceFeature[]) feats[i]).length;
scores[i] = featureCount;
- // jalview.bin.Console.errPrintln("Sorting on Density: seq "+seqs[i].getName()+
+ // jalview.bin.Console.errPrintln("Sorting on Density: seq
+ // "+seqs[i].getName()+
// " Feats: "+featureCount+" Score : "+scores[i]);
}
QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
if (translated == null || !(aaRes == translated.charAt(0)))
{
// debug
- // jalview.bin.Console.outPrintln(("Mismatch at " + i + "/" + aaResidue + ": "
+ // jalview.bin.Console.outPrintln(("Mismatch at " + i + "/" + aaResidue
+ // + ": "
// + codon + "(" + translated + ") != " + aaRes));
return false;
}
* unmapped position; treat like a gap
*/
sourceGapMappedLength += ratio;
- // jalview.bin.Console.errPrintln("Can't align: no codon mapping to residue "
+ // jalview.bin.Console.errPrintln("Can't align: no codon mapping to
+ // residue "
// + sourceDsPos + "(" + sourceChar + ")");
// return;
continue;
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
- jalview.bin.Console.errPrintln("Wrong alignment type in alignProteinAsDna");
+ jalview.bin.Console
+ .errPrintln("Wrong alignment type in alignProteinAsDna");
return 0;
}
List<SequenceI> unmappedProtein = new ArrayList<>();
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
- jalview.bin.Console.errPrintln("Wrong alignment type in alignProteinAsDna");
+ jalview.bin.Console
+ .errPrintln("Wrong alignment type in alignProteinAsDna");
return 0;
}
// todo: implement this
* @param alignment
* the alignment to add them to
* @param selectionGroup
- * current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
+ * current selection group - may be null, if provided then any added
+ * annotation will be trimmed to just those columns in the selection
+ * group
*/
public static void addReferenceAnnotations(
Map<SequenceI, List<AlignmentAnnotation>> annotations,
* @param seq
* @param ann
* @param selectionGroup
- * current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
+ * current selection group - may be null, if provided then any added
+ * annotation will be trimmed to just those columns in the selection
+ * group
* @return annotation added to {@code seq and {@code alignment}
*/
public static AlignmentAnnotation addReferenceAnnotationTo(
fromRange[i + 1]);
if (range == null)
{
- jalview.bin.Console.errPrintln("Error in mapping " + seqMap + " from "
- + fromSeq.getName());
+ jalview.bin.Console.errPrintln("Error in mapping " + seqMap
+ + " from " + fromSeq.getName());
return false;
}
int fromCol = fromSeq.findIndex(fromRange[i]);
/**
* compute cosine distance matrix for a given contact matrix and create a
* UPGMA tree
+ *
* @param cm
- * @param cosineOrDifference false - dot product : true - L1
+ * @param cosineOrDifference
+ * false - dot product : true - L1
*/
public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa,
ContactMatrixI cm, boolean cosineOrDifference)
this.av = av;
this.aa = aa;
this.cm = cm;
- mode = (cosineOrDifference) ? 1 :0;
+ mode = (cosineOrDifference) ? 1 : 0;
calculate(cm);
}
-
public void calculate(ContactMatrixI cm)
{
this.cm = cm;
// compute distance matrix element
ContactListI ith = cm.getContactList(i);
distances.setValue(i, i, 0);
- if (ith==null)
+ if (ith == null)
{
continue;
}
}
if (dataset.getSequences() == null)
{
- jalview.bin.Console.errPrintln("Empty dataset sequence set - NO VECTOR");
+ jalview.bin.Console
+ .errPrintln("Empty dataset sequence set - NO VECTOR");
return false;
}
List<SequenceI> ds = dataset.getSequences();
InputStream is = getClass().getResourceAsStream(fileName);
if (is == null)
{
- jalview.bin.Console.errPrintln("Resource file not found: " + fileName);
+ jalview.bin.Console
+ .errPrintln("Resource file not found: " + fileName);
return;
}
BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
InputStream is = getClass().getResourceAsStream(fileName);
if (is == null)
{
- jalview.bin.Console.errPrintln("Resource file not found: " + fileName);
+ jalview.bin.Console
+ .errPrintln("Resource file not found: " + fileName);
return;
}
BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
final int close = basePair.getBP3();
// jalview.bin.Console.outPrintln("open " + open + " close " + close);
- // jalview.bin.Console.outPrintln("lastclose " + lastclose + " lastopen " + lastopen);
+ // jalview.bin.Console.outPrintln("lastclose " + lastclose + " lastopen "
+ // + lastopen);
// we're moving from right to left based on closing pair
/*
{
int popen = bps.get(j).getBP5();
- // jalview.bin.Console.outPrintln("j " + j + " popen " + popen + " lastopen "
+ // jalview.bin.Console.outPrintln("j " + j + " popen " + popen + "
+ // lastopen "
// +lastopen + " open " + open);
if ((popen < lastopen) && (popen > open))
{
{
// if (_lycount<_lylimit)
// {
- // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than number of
+ // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than
+ // number of
// nodes.");
// }
if (nd == null)
if ((nd.left() == null) && (nd.right() == null))
{
- // TODO FIX FOR COLUMN TREES
- jalview.bin.Console.outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
+ // TODO FIX FOR COLUMN TREES
+ jalview.bin.Console
+ .outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
jalview.bin.Console.outPrintln("Dist " + nd.dist);
jalview.bin.Console.outPrintln("Boot " + nd.getBootstrap());
}
}
else
{
- jalview.bin.Console.outPrintln(" name = " + ((SequenceI) nd.element()).getName());
+ jalview.bin.Console.outPrintln(
+ " name = " + ((SequenceI) nd.element()).getName());
}
jalview.bin.Console.outPrintln(
{
// if (_lycount<_lylimit)
// {
- // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than number of
+ // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than
+ // number of
// nodes.");
// }
if (nd == null)
ScoreModelI sm2 = models.get(sm.getName());
if (sm2 != null)
{
- jalview.bin.Console.errPrintln("Warning: replacing score model " + sm2.getName());
+ jalview.bin.Console.errPrintln(
+ "Warning: replacing score model " + sm2.getName());
}
models.put(sm.getName(), sm);
}
/**
* Configure the Graphics canvas and render options for the renderer
- * @param g - the canvas to render to
- * @param renderGaps - when true, gap characters will be included when rendered
- *
+ *
+ * @param g
+ * - the canvas to render to
+ * @param renderGaps
+ * - when true, gap characters will be included when rendered
+ *
*/
void prepare(Graphics g, boolean renderGaps);
/**
*
- * @return heteroatoms in a form suitable for display and passing to command generator to display hetatms
+ * @return heteroatoms in a form suitable for display and passing to command
+ * generator to display hetatms
*/
- default List<String> getHetatms() {
+ default List<String> getHetatms()
+ {
return Collections.EMPTY_LIST;
}
urlLink = new UrlLink(link);
} catch (Exception foo)
{
- jalview.bin.Console.errPrintln("Exception for URLLink '" + link + "': "
- + foo.getMessage());
+ jalview.bin.Console.errPrintln("Exception for URLLink '" + link
+ + "': " + foo.getMessage());
continue;
}
{
if (viewport.applet == null)
{
- jalview.bin.Console.outPrintln("Not running as applet - no browser available.");
+ jalview.bin.Console
+ .outPrintln("Not running as applet - no browser available.");
}
else
{
}
if (viewer == null)
{
- jalview.bin.Console.errPrintln("Can't use this object as a structure viewer:"
- + jmolviewer.getClass());
+ jalview.bin.Console
+ .errPrintln("Can't use this object as a structure viewer:"
+ + jmolviewer.getClass());
return null;
}
SequenceI[] seqs = null;
}
if (protocol == null)
{
- jalview.bin.Console.errPrintln("Couldn't work out protocol to open structure: "
- + pdb.getId());
+ jalview.bin.Console
+ .errPrintln("Couldn't work out protocol to open structure: "
+ + pdb.getId());
return;
}
}
.setMapping(seqs, chains, pdb.getFile(), protocol,
null) == null)
{
- jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile() + " ("
- + protocol + ") to any sequences");
+ jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile()
+ + " (" + protocol + ") to any sequences");
}
return;
}
SequenceI[][] seqs, String[][] chains, String[] protocols)
{
// TODO Auto-generated method stub
- jalview.bin.Console.errPrintln("Aligned Structure View: Not yet implemented.");
+ jalview.bin.Console
+ .errPrintln("Aligned Structure View: Not yet implemented.");
}
/**
if ((hextent + x) > width)
{
- jalview.bin.Console.errPrintln("hextent was " + hextent + " and x was " + x);
+ jalview.bin.Console
+ .errPrintln("hextent was " + hextent + " and x was " + x);
x = width - hextent;
}
validate();
sliderValueChanged();
- // jalview.bin.Console.outPrintln("blob done "+ (System.currentTimeMillis()-start));
+ // jalview.bin.Console.outPrintln("blob done "+
+ // (System.currentTimeMillis()-start));
}
void sliderValueChanged()
{
char s = nextSeq.getCharAt(cursorX);
- sr.drawCursor(g,s, (cursorX - startRes) * avcharWidth,
+ sr.drawCursor(g, s, (cursorX - startRes) * avcharWidth,
offset + ((i - startSeq) * avcharHeight));
}
}
{
if (av.getAlignment() == null)
{
- jalview.bin.Console.outPrintln("Selection message: alignviewport av SeqSetId="
- + av.getSequenceSetId() + " ViewId=" + av.getViewId()
- + " 's alignment is NULL! returning immediatly.");
+ jalview.bin.Console.outPrintln(
+ "Selection message: alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId="
+ + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
return;
}
sgroup = seqsel.intersect(av.getAlignment(),
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
{
if (debug)
{
- jalview.bin.Console.errPrintln("Selecting region using separator string '"
- + separator + "'");
+ jalview.bin.Console
+ .errPrintln("Selecting region using separator string '"
+ + separator + "'");
}
}
// deparse fields
}
if (debug)
{
- jalview.bin.Console.errPrintln("Range '" + cl + "' deparsed as [" + from
- + "," + to + "]");
+ jalview.bin.Console.errPrintln("Range '" + cl
+ + "' deparsed as [" + from + "," + to + "]");
}
}
else
}
else
{
- jalview.bin.Console.errPrintln("ERROR: Invalid Point selection '" + cl
- + "' deparsed as [" + r + "]");
+ jalview.bin.Console
+ .errPrintln("ERROR: Invalid Point selection '" + cl
+ + "' deparsed as [" + r + "]");
}
}
}
+ ((af == null) ? "All frames"
: "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
- + " listeners in total.");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
+ ((af == null) ? "All frames"
: "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
- + " listeners in total.");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
.addStructureViewerListener(mol);
if (debug)
{
- jalview.bin.Console.errPrintln("Added a javascript structure viewer listener '"
- + listener + "'");
- jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
- + " listeners in total.");
+ jalview.bin.Console
+ .errPrintln("Added a javascript structure viewer listener '"
+ + listener + "'");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
rprt = debug;
if (debug)
{
- jalview.bin.Console.errPrintln("Removed listener '" + listener + "'");
+ jalview.bin.Console
+ .errPrintln("Removed listener '" + listener + "'");
}
}
else
}
if (rprt)
{
- jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
- + " listeners in total.");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
}
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln("Ignoring invalid residue number string '"
- + pdbResNum + "'");
+ jalview.bin.Console
+ .errPrintln("Ignoring invalid residue number string '"
+ + pdbResNum + "'");
}
}
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Couldn't parse integer arguments (topRow='"
- + topRow + "' and leftHandColumn='" + leftHandColumn
- + "')");
+ jalview.bin.Console
+ .errPrintln("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='"
+ + leftHandColumn + "')");
ex.printStackTrace();
}
}
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Couldn't parse integer arguments (topRow='"
- + topRow + "')");
+ jalview.bin.Console
+ .errPrintln("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
ex.printStackTrace();
}
JSObject scriptObject = JSObject.getWindow(this);
if (debug && scriptObject != null)
{
- jalview.bin.Console.errPrintln("Applet has Javascript callback support.");
+ jalview.bin.Console
+ .errPrintln("Applet has Javascript callback support.");
}
} catch (Exception ex)
separator = sep;
if (debug)
{
- jalview.bin.Console.errPrintln("Separator set to '" + separator + "'");
+ jalview.bin.Console
+ .errPrintln("Separator set to '" + separator + "'");
}
}
else
{
if (tries > 0)
{
- jalview.bin.Console.errPrintln("LiveConnect request thread going to sleep.");
+ jalview.bin.Console
+ .errPrintln("LiveConnect request thread going to sleep.");
}
try
{
;
if (tries++ > 0)
{
- jalview.bin.Console.errPrintln("LiveConnect request thread woken up.");
+ jalview.bin.Console
+ .errPrintln("LiveConnect request thread woken up.");
}
try
{
"Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Exception when executing _oninit callback '"
- + initjscallback + "'.");
+ jalview.bin.Console
+ .errPrintln("Exception when executing _oninit callback '"
+ + initjscallback + "'.");
e.printStackTrace();
}
}
{
if (debug)
{
- jalview.bin.Console.errPrintln("Prepended document base '" + documentBase
- + "' to make: '" + withDocBase + "'");
+ jalview.bin.Console.errPrintln("Prepended document base '"
+ + documentBase + "' to make: '" + withDocBase + "'");
}
protocol = DataSourceType.URL;
return withDocBase;
return rtn;
} catch (Exception ex)
{
- jalview.bin.Console.outPrintln("Exception checking resources: " + f + " " + ex);
+ jalview.bin.Console.outPrintln(
+ "Exception checking resources: " + f + " " + ex);
return false;
}
}
this.separator = separator;
if (debug)
{
- jalview.bin.Console.errPrintln("Default Separator now: '" + separator + "'");
+ jalview.bin.Console
+ .errPrintln("Default Separator now: '" + separator + "'");
}
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- jalview.bin.Console.errPrintln("Couldn't parse '" + colprop + "' as a colour for "
- + colparam);
+ jalview.bin.Console.errPrintln("Couldn't parse '" + colprop
+ + "' as a colour for " + colparam);
}
return (col == null) ? defcolour : col;
}
DataSourceType protocol = null;
try
{
- jalview.bin.Console.outPrintln("Loading thread started with:\n>>file\n" + file
- + ">>endfile");
+ jalview.bin.Console
+ .outPrintln("Loading thread started with:\n>>file\n" + file
+ + ">>endfile");
// This might throw a security exception in certain browsers
// Netscape Communicator for instance.
try
}
else
{
- jalview.bin.Console.outPrintln("User specified Format is " + format);
+ jalview.bin.Console
+ .outPrintln("User specified Format is " + format);
}
AlignmentI al = null;
try
//
// for (int s = 0; s < command.seqs.length; s++)
// {
- // jalview.bin.Console.outPrintln("pos: "+command.position+" number: "+command.number);
+ // jalview.bin.Console.outPrintln("pos: "+command.position+" number:
+ // "+command.number);
// command.seqs[s].insertCharAt(command.position, command.number,'A');
// }
//
}
else
{
- jalview.bin.Console.errPrintln("Can't undo edit action " + action);
+ jalview.bin.Console
+ .errPrintln("Can't undo edit action " + action);
// throw new IllegalStateException("Can't undo edit action " +
// action);
}
ds.setSequenceFeatures(dna.getSequenceFeatures());
// dnaSeqs[i] = ds;
ssm.fromSeq = ds;
- jalview.bin.Console.outPrintln("Realised mapped sequence " + ds.getName());
+ jalview.bin.Console
+ .outPrintln("Realised mapped sequence " + ds.getName());
}
}
}
if (cm == null && _aa.sequenceRef != null)
{
cm = _aa.sequenceRef.getContactMatrixFor(_aa);
- if (cm == null && _aa.sequenceRef.getDatasetSequence()!=null)
+ if (cm == null && _aa.sequenceRef.getDatasetSequence() != null)
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
@Override
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
- if (_aa.annotations==null || column>=_aa.annotations.length || column<0)
+ if (_aa.annotations == null || column >= _aa.annotations.length
+ || column < 0)
{
return null;
}
}
if (to_column >= getContactHeight())
{
- to_column = getContactHeight()-1;
+ to_column = getContactHeight() - 1;
}
ContactRange cr = new ContactRange();
cr.setFrom_column(from_column);
}
}
}
- if (tot > 0 && to_column>from_column)
+ if (tot > 0 && to_column > from_column)
{
cr.setMean(tot / (1 + to_column - from_column));
}
{
if (contactmaps != null && contactmaps.size() > 0)
{
- // defensive copy, and return non redundant set of ContactMatrixI instances
+ // defensive copy, and return non redundant set of ContactMatrixI
+ // instances
return new HashSet<ContactMatrixI>(contactmaps.values());
}
return Collections.EMPTY_LIST;
import jalview.bin.Console;
-public abstract class ContactMatrix extends GroupSetHolder implements ContactMatrixI
+public abstract class ContactMatrix extends GroupSetHolder
+ implements ContactMatrixI
{
/**
* are contacts reflexive ?
}
});
}
+
private Float getFloatElementAt(int column, int p)
{
-
+
List<Float> clist;
Float cl = null;
if (symmetric)
}
return cl;
}
+
@Override
public double getElementAt(int column, int row)
{
Float cl = getFloatElementAt(column, row);
- if (cl!=null)
+ if (cl != null)
{
return cl;
}
- throw(new RuntimeException("Out of Bounds "+column+","+row));
+ throw (new RuntimeException("Out of Bounds " + column + "," + row));
}
+
@Override
public float getMin()
{
{
return "Contact Matrix";
}
+
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
for (int c = 0; c < cm.getWidth(); c++)
{
ContactListI cl = cm.getContactList(c);
- long lastsb=-1;
+ long lastsb = -1;
if (cl != null)
{
for (int h = 0; h <= cl.getContactHeight(); h++)
{
if (sb.length() > 0)
{
- if (sb.length()-lastsb>320)
+ if (sb.length() - lastsb > 320)
{
// newline
sb.append('\n');
- lastsb=sb.length();
- } else {
+ lastsb = sb.length();
+ }
+ else
+ {
sb.append('\t');
}
}
int rows)
{
float[][] vals = new float[cols][rows];
- StringTokenizer tabsep = new StringTokenizer(values, "" + '\t'+'\n');
+ StringTokenizer tabsep = new StringTokenizer(values, "" + '\t' + '\n');
int c = 0, r = 0;
while (tabsep.hasMoreTokens())
{
String getType();
int getWidth();
+
int getHeight();
+
public GroupSetI getGroupSet();
/// proxy methods to simplify use of the interface
void setGroupSet(GroupSet makeGroups);
- default void randomlyReColourGroups() {
+ default void randomlyReColourGroups()
+ {
if (hasGroupSet())
{
GroupSetI groups = getGroupSet();
- for (BitSet group:groups.getGroups())
+ for (BitSet group : groups.getGroups())
{
groups.setColorForGroup(group, ColorUtils.getARandomColor());
}
}
}
}
-
+
/**
- * look up the colour for a column in the associated contact matrix
+ * look up the colour for a column in the associated contact matrix
+ *
* @return Color.white or assigned colour
*/
default Color getGroupColorForPosition(int column)
if (hasGroupSet())
{
GroupSetI groups = getGroupSet();
- for (BitSet gp:groups.getGroups())
+ for (BitSet gp : groups.getGroups())
{
if (gp.get(column))
{
/**
* direct access to column and row position of matrix
-
- * Implementations are allowed to throw
- * RunTimeExceptions if _column/i are out of bounds
+ *
+ * Implementations are allowed to throw RunTimeExceptions if _column/i are out
+ * of bounds
*
* @param column
* @param row
* @return
*/
double getElementAt(int column, int row);
-
+
}
public static boolean isPrimaryCandidate(String ucversion)
{
- if (ucversion==null)
+ if (ucversion == null)
{
// Null/empty version is not a real reference ?
return false;
package jalview.datamodel;
-public class FloatContactMatrix extends GroupSetHolder implements ContactMatrixI
+public class FloatContactMatrix extends GroupSetHolder
+ implements ContactMatrixI
{
int maxrow = 0, maxcol = 0;
-
float[][] elements;
float maxscore;
-
public FloatContactMatrix(float[][] matrix)
{
maxcol = 0;
{
return makeGroups(matrix, autoCut, 0, autoCut);
}
- public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto, float thresh,
- boolean abs)
+
+ public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto,
+ float thresh, boolean abs)
{
AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
matrix, true);
nodegroups.add(clusterer.getTopNode());
}
}
-
+
List<BitSet> groups = new ArrayList<>();
for (BinaryNode root : nodegroups)
{
/**
*
* @param seq
- * @param from - first position to highlight
- * @param to - last position to highlight (assumed higher than from)
- * @return true iff from-to intersects or marks positions either side of start/end
+ * @param from
+ * - first position to highlight
+ * @param to
+ * - last position to highlight (assumed higher than from)
+ * @return true iff from-to intersects or marks positions either side of
+ * start/end
*/
boolean adjacent(SequenceI seq, int from, int to);
}
\ No newline at end of file
* One match consists of a sequence reference, start and end positions.
* Discontiguous ranges in a sequence require two or more Match objects.
*/
- public class Match implements SearchResultMatchI, Comparable<SearchResultMatchI>
+ public class Match
+ implements SearchResultMatchI, Comparable<SearchResultMatchI>
{
final SequenceI sequence;
{
return (sequence == seq && start <= from && end >= to);
}
+
@Override
public boolean adjacent(SequenceI seq, int from, int to)
{
- return (sequence == seq && ((start <= from && end >= to) || (from<=(end+1) && to >=(end+1)) || (from<=(start-1) && to>=(start-1))));
+ return (sequence == seq && ((start <= from && end >= to)
+ || (from <= (end + 1) && to >= (end + 1))
+ || (from <= (start - 1) && to >= (start - 1))));
}
@Override
public int compareTo(SearchResultMatchI o)
{
- if (start<o.getStart())
+ if (start < o.getStart())
{
return -1;
}
{
return +1;
}
- if (sequence!=o.getSequence())
+ if (sequence != o.getSequence())
{
- int hashc =sequence.hashCode(),oseq=o.getSequence().hashCode();
+ int hashc = sequence.hashCode(), oseq = o.getSequence().hashCode();
return (hashc < oseq) ? -1 : 1;
}
return 0;
}
-
+
}
@Override
count = beforeCount + 1;
}
}
-
@Override
public boolean appendResult(SequenceI sequence, int start, int end)
{
Match m = new Match(sequence, start, end);
-
- boolean appending=false;
-
- // we dynamically maintain an interval to add as we test each range in the list
-
- int cstart=start,cend=end;
- List<SearchResultMatchI> toRemove=new ArrayList<>();
- for (SearchResultMatchI thatm:matches)
+
+ boolean appending = false;
+
+ // we dynamically maintain an interval to add as we test each range in the
+ // list
+
+ int cstart = start, cend = end;
+ List<SearchResultMatchI> toRemove = new ArrayList<>();
+ for (SearchResultMatchI thatm : matches)
{
- if (thatm.getSequence()==sequence)
+ if (thatm.getSequence() == sequence)
{
- if (thatm.contains(sequence,cstart,cend))
+ if (thatm.contains(sequence, cstart, cend))
{
- // found a match containing the current range. nothing else to do except report if we operated on the list
+ // found a match containing the current range. nothing else to do
+ // except report if we operated on the list
return appending;
}
if (thatm.adjacent(sequence, cstart, cend))
start = Math.min(m.start, thatm.getStart());
end = Math.max(m.end, thatm.getEnd());
// and check if we keep or remove the old one
- if (thatm.getStart()!=start || thatm.getEnd()!=end)
- {
+ if (thatm.getStart() != start || thatm.getEnd() != end)
+ {
toRemove.add(thatm);
count--;
cstart = start;
cend = end;
- appending=true;
- } else {
+ appending = true;
+ }
+ else
+ {
return false;
}
}
}
matches.removeAll(toRemove);
{
- matches.add(new Match(sequence,cstart,cend));
+ matches.add(new Match(sequence, cstart, cend));
count++;
}
return appending;
}
+
@Override
public boolean involvesSequence(SequenceI sequence)
{
else
{
// debug
- // jalview.bin.Console.errPrintln("Outwith bounds!" + matchStart+">"+end +" or "
+ // jalview.bin.Console.errPrintln("Outwith bounds!" +
+ // matchStart+">"+end +" or "
// + matchEnd+"<"+start);
}
}
*/
void addResult(SequenceI seq, int[] positions);
-
/**
* Adds the given start/end region to this search result. If sequence already
* has a search result and the range is adjacent to already highlighted
import jalview.util.MapList;
import jalview.ws.datamodel.alphafold.MappableContactMatrix;
+
/**
* Dummy contact matrix based on sequence distance
*
implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
private int width = 0;
public SeqDistanceContactMatrix(int width)
{
return width;
}
+
@Override
public double getElementAt(int _column, int i)
{
return Math.abs(_column - i);
}
+
@Override
protected SeqDistanceContactMatrix newMappableContactMatrix(
SequenceI newRefSeq, MapList newFromMapList)
// only copy the given annotation
AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
ContactMatrixI cm = seq.getContactMatrixFor(sqann[i]);
- if (cm!=null)
+ if (cm != null)
{
addContactListFor(newann, cm);
}
}
}
// all matrices should have been transferred. so we clear the local holder
- _cmholder=null;
+ _cmholder = null;
}
return datasetSequence;
}
}
// transfer from entry to sequence
// if entry has a description and sequence doesn't, then transfer
- if (entry.getDescription()!=null && (description==null || description.trim().length()==0))
+ if (entry.getDescription() != null
+ && (description == null || description.trim().length() == 0))
{
description = entry.getDescription();
}
-
+
// transfer any new features from entry onto sequence
if (entry.getSequenceFeatures() != null)
{
private ContactMapHolderI getContactMapHolder()
{
- if (datasetSequence!=null) {
- return ((Sequence)datasetSequence).getContactMapHolder();
+ if (datasetSequence != null)
+ {
+ return ((Sequence) datasetSequence).getContactMapHolder();
}
- if (_cmholder==null)
+ if (_cmholder == null)
{
- _cmholder=new ContactMapHolder();
+ _cmholder = new ContactMapHolder();
}
return _cmholder;
}
+
@Override
public Collection<ContactMatrixI> getContactMaps()
{
public AlignmentAnnotation addContactList(ContactMatrixI cm)
{
AlignmentAnnotation aa;
-
+
if (datasetSequence != null)
{
aa = datasetSequence.addContactList(cm);
aa = new AlignmentAnnotation(aa);
aa.restrict(start, end);
aa.adjustForAlignment();
- getContactMapHolder().addContactListFor(aa,cm);
+ getContactMapHolder().addContactListFor(aa, cm);
addAlignmentAnnotation(aa);
return aa;
}
-
+
// construct new annotation for matrix on dataset sequence
aa = getContactMapHolder().addContactList(cm);
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
- ContactMatrixI cm = seq.getContactMatrixFor(seq.getAnnotation()[a]);
- if (cm!=null)
+ ContactMatrixI cm = seq
+ .getContactMatrixFor(seq.getAnnotation()[a]);
+ if (cm != null)
{
seqs[ipos].addContactListFor(newannot, cm);
}
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
- jalview.bin.Console.outPrintln("Out of memory loading groups: " + err);
+ jalview.bin.Console
+ .outPrintln("Out of memory loading groups: " + err);
}
return upd;
}
/**
* Derive a sequence (using this one's dataset or as the dataset)
*
- * @return duplicate sequence and any annotation present with valid dataset sequence
+ * @return duplicate sequence and any annotation present with valid dataset
+ * sequence
*/
public SequenceI deriveSequence();
SequenceFeature sf = contactFeatureEnds.get(index);
if (!sf.isContactFeature())
{
- jalview.bin.Console.errPrintln("Error! non-contact feature type " + sf.getType()
- + " in contact features list");
+ jalview.bin.Console.errPrintln("Error! non-contact feature type "
+ + sf.getType() + " in contact features list");
index++;
continue;
}
SequenceFeature sf = contactFeatureStarts.get(index);
if (!sf.isContactFeature())
{
- jalview.bin.Console.errPrintln("Error! non-contact feature " + sf.toString()
- + " in contact features list");
+ jalview.bin.Console.errPrintln("Error! non-contact feature "
+ + sf.toString() + " in contact features list");
index++;
continue;
}
String type = sf.getType();
if (type == null)
{
- jalview.bin.Console.errPrintln("Feature type may not be null: " + sf.toString());
+ jalview.bin.Console
+ .errPrintln("Feature type may not be null: " + sf.toString());
return false;
}
return true;
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln("Bad integers in description " + description);
+ jalview.bin.Console
+ .errPrintln("Bad integers in description " + description);
}
}
return false;
ids, -1, MODE_MAP, null);
} catch (IOException | ParseException e)
{
- jalview.bin.Console.errPrintln("Error parsing " + identifier + " lookup response "
- + e.getMessage());
+ jalview.bin.Console.errPrintln("Error parsing " + identifier
+ + " lookup response " + e.getMessage());
return null;
}
}
return (parseAssemblyMappingResponse(url));
} catch (Throwable t)
{
- jalview.bin.Console.outPrintln("Error calling " + url + ": " + t.getMessage());
+ jalview.bin.Console
+ .outPrintln("Error calling " + url + ": " + t.getMessage());
return null;
}
}
return null;
} catch (Throwable t)
{
- jalview.bin.Console.outPrintln("Error calling " + url + ": " + t.getMessage());
+ jalview.bin.Console
+ .outPrintln("Error calling " + url + ": " + t.getMessage());
return null;
}
}
* note: a GET request for an invalid id returns an error code e.g. 415
* but POST request returns 200 and an empty Fasta response
*/
- jalview.bin.Console.errPrintln("Response code " + responseCode);// + " for " + url);
+ jalview.bin.Console.errPrintln("Response code " + responseCode);// + " for
+ // " +
+ // url);
return null;
}
}
} catch (NumberFormatException | InterruptedException e)
{
- jalview.bin.Console.errPrintln("Error handling Retry-After: " + e.getMessage());
+ jalview.bin.Console.errPrintln(
+ "Error handling Retry-After: " + e.getMessage());
}
}
}
}
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln("Error in REST version: " + e.toString());
+ jalview.bin.Console
+ .errPrintln("Error in REST version: " + e.toString());
}
/*
.getSequenceRecords(accId);
if (protein == null || protein.getHeight() == 0)
{
- jalview.bin.Console.outPrintln("No protein product found for " + accId);
+ jalview.bin.Console
+ .outPrintln("No protein product found for " + accId);
return;
}
SequenceI proteinSeq = protein.getSequenceAt(0);
seq.addDBRef(xrefs.get(i));
}
- // jalview.bin.Console.outPrintln("primaries are " + seq.getPrimaryDBRefs().toString());
+ // jalview.bin.Console.outPrintln("primaries are " +
+ // seq.getPrimaryDBRefs().toString());
/*
* and add a reference to itself
*/
result.add(sequence);
} catch (ParseException | IOException e)
{
- jalview.bin.Console.errPrintln("Error processing JSON response: " + e.toString());
+ jalview.bin.Console.errPrintln(
+ "Error processing JSON response: " + e.toString());
// ignore
}
// Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
if (regions.isEmpty())
{
- jalview.bin.Console.outPrintln("Failed to identify target sequence for " + accId
- + " from genomic features");
+ jalview.bin.Console
+ .outPrintln("Failed to identify target sequence for " + accId
+ + " from genomic features");
return null;
}
boolean result = transferFeatures(sfs, targetSequence, mapping,
accessionId);
- // jalview.bin.Console.outPrintln("transferFeatures (" + (sfs.size()) + " --> "
+ // jalview.bin.Console.outPrintln("transferFeatures (" + (sfs.size()) + "
+ // --> "
// + targetSequence.getFeatures().getFeatureCount(true) + ") to "
// + targetSequence.getName() + " took "
// + (System.currentTimeMillis() - start) + "ms");
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(cmd))
{
- jmolScript(cmd + "\n",command.isWaitNeeded());
+ jmolScript(cmd + "\n", command.isWaitNeeded());
}
jmolHistory(true);
lastCommand = cmd;
// End StructureListener
// //////////////////////////
-
+
////////////////////////////
// HETATM get
//
-
+
@Override
- public Map<String,String> getHetatmNames()
+ public Map<String, String> getHetatmNames()
{
- HashMap<String,String> hetlist=new HashMap();
- for (int mc=0;mc<jmolViewer.ms.mc; mc++)
+ HashMap<String, String> hetlist = new HashMap();
+ for (int mc = 0; mc < jmolViewer.ms.mc; mc++)
{
- Map<String,String> hets = jmolViewer.ms.getHeteroList(mc);
- if (hets!=null)
+ Map<String, String> hets = jmolViewer.ms.getHeteroList(mc);
+ if (hets != null)
{
hetlist.putAll(hets);
}
}
//
////////////////////////////
-
+
@Override
public float[][] functionXY(String functionName, int x, int y)
{
jmolScript(resetLastRes.toString());
resetLastRes.setLength(0);
}
- StringBuilder highlightCommands=null;
+ StringBuilder highlightCommands = null;
for (AtomSpec atom : atoms)
{
- StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
- atom.getChain(), atom.getPdbFile());
- if (thisAtom!=null) {
- if (highlightCommands==null)
+ StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(),
+ atom.getPdbResNum(), atom.getChain(), atom.getPdbFile());
+ if (thisAtom != null)
+ {
+ if (highlightCommands == null)
+ {
+ highlightCommands = thisAtom;
+ }
+ else
{
- highlightCommands=thisAtom;
- } else {
highlightCommands.append(thisAtom);
}
}
}
- if (highlightCommands!=null)
+ if (highlightCommands != null)
{
jmolHistory(false);
jmolScript(highlightCommands.toString());
}
// jmol/ssm only
- private StringBuilder highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ private StringBuilder highlightAtom(int atomIndex, int pdbResNum,
+ String chain, String pdbfile)
{
String modelId = getModelIdForFile(pdbfile);
if (modelId.isEmpty())
lastMessage = strInfo;
if (data != null)
{
- jalview.bin.Console.errPrintln("Ignoring additional hover info: " + data
- + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+ jalview.bin.Console.errPrintln(
+ "Ignoring additional hover info: " + data + " (other info: '"
+ + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
}
*/
if (strData != null)
{
- jalview.bin.Console.errPrintln("Ignoring additional pick data string " + strData);
+ jalview.bin.Console.errPrintln(
+ "Ignoring additional pick data string " + strData);
}
int chainSeparator = strInfo.indexOf(":");
int p = 0;
}
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Squashed Jmol callback handler error:");
+ jalview.bin.Console
+ .errPrintln("Squashed Jmol callback handler error:");
e.printStackTrace();
}
}
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
- jalview.bin.Console.errPrintln("Ignoring set-callback request to associate "
- + callbackType + " with function " + callbackFunction);
+ jalview.bin.Console
+ .errPrintln("Ignoring set-callback request to associate "
+ + callbackType + " with function " + callbackFunction);
}
String buttonsToShow)
{
- jalview.bin.Console.errPrintln("Allocating Jmol Viewer: " + commandOptions);
+ jalview.bin.Console
+ .errPrintln("Allocating Jmol Viewer: " + commandOptions);
if (commandOptions == null)
{
console = createJmolConsole(consolePanel, buttonsToShow);
} catch (Throwable e)
{
- jalview.bin.Console.errPrintln("Could not create Jmol application console. "
- + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("Could not create Jmol application console. "
+ + e.getMessage());
e.printStackTrace();
}
if (consolePanel != null)
/*
* https://chemapps.stolaf.edu/jmol/docs/#writemodel
*/
- StructureCommand sc = new StructureCommand("write STATE \"" + filepath + "\"");
+ StructureCommand sc = new StructureCommand(
+ "write STATE \"" + filepath + "\"");
sc.setWaitNeeded(true);
return sc;
}
return new StructureCommand(
"load FILES \"" + Platform.escapeBackslashes(file) + "\"");
}
+
@Override
public StructureCommandI restoreSession(String filePath)
{
- return new StructureCommand(
- "restore STATE \"" + Platform.escapeBackslashes(filePath) + "\"");
+ return new StructureCommand("restore STATE \""
+ + Platform.escapeBackslashes(filePath) + "\"");
}
@Override
public List<StructureCommandI> showHetatms(List<String> toShow)
{
// always clear the current hetero cpk display
-
+
StringBuilder sb = new StringBuilder();
sb.append("select hetero; cpk off;");
-
+
if (toShow != null && !toShow.isEmpty())
{
// select what was requested
// and show as
sb.append("; cpk;");
}
-
+
return Arrays.asList(new StructureCommand(sb.toString()));
}
+
/**
* Obsolete method, only referenced from
* jalview.javascript.MouseOverStructureListener
{
super(fp, doXferSettings);
}
+
public JmolParser(FileParse fp) throws IOException
{
super(fp);
{
int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
+ Annotation asecstr[] = new Annotation[length
+ + (firstResNum - sq.getStart())];
for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
}
else
{
- jalview.bin.Console.errPrintln("Unexpected chimeraNotification: " + message);
+ jalview.bin.Console
+ .errPrintln("Unexpected chimeraNotification: " + message);
}
}
}
*/
protected void processModelChanged(String message)
{
- // jalview.bin.Console.outPrintln(message + " (not implemented in Jalview)");
+ // jalview.bin.Console.outPrintln(message + " (not implemented in
+ // Jalview)");
}
/**
executeCommand(false, null, command);
} catch (IOException e)
{
- jalview.bin.Console.errPrintln("Sending commands to Chimera via file failed with "
- + e.getMessage());
+ jalview.bin.Console.errPrintln(
+ "Sending commands to Chimera via file failed with "
+ + e.getMessage());
}
}
int x = 0;
for (FTSDataColumnI field : allFTSDataColumns)
{
- // jalview.bin.Console.outPrintln("allFTSDataColumns==" + allFTSDataColumns);
+ // jalview.bin.Console.outPrintln("allFTSDataColumns==" +
+ // allFTSDataColumns);
if (field.getName().equalsIgnoreCase("all"))
{
continue;
data[x++] = new Object[] { ftsRestClient
.getAllDefaultDisplayedFTSDataColumns().contains(field),
field.getName(), field.getGroup() };
- // jalview.bin.Console.outPrintln(" PUIS " + field.getName() + " ET AUSSI " +
+ // jalview.bin.Console.outPrintln(" PUIS " + field.getName() + " ET
+ // AUSSI " +
// field.getGroup() + "X = " + x);
break;
case STRUCTURE_CHOOSER:
Map<String, Object> jsonObj = null;
String responseString = null;
- jalview.bin.Console.outPrintln("query >>>>>>> " + pdbRestRequest.toString());
+ jalview.bin.Console
+ .outPrintln("query >>>>>>> " + pdbRestRequest.toString());
if (!isMocked())
{
{
return (String) getField(Model_id);
}
-
+
public String getConfidenceScoreType()
{
return (String) getField(Confidence_Score_Type);
}
+
public String getConfidenceScoreVersion()
{
return (String) getField(Confidence_Score_Version);
String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
? " "
: tdbJsonStructure.get(field.getCode()).toString();
- // jalview.bin.Console.outPrintln("Field : " + field + " Data : " + fieldData);
+ // jalview.bin.Console.outPrintln("Field : " + field + " Data : " +
+ // fieldData);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
} catch (Exception e)
{
// e.printStackTrace();
- jalview.bin.Console.outPrintln("offending value:" + fieldData + fieldData);
+ jalview.bin.Console
+ .outPrintln("offending value:" + fieldData + fieldData);
}
}
}
}
mtch = idm.findAllIdMatches(pdbfn);
}
- FileFormatI type=null;
+ FileFormatI type = null;
if (mtch != null)
{
try
}
// File wasn't named like one of the sequences or wasn't a PDB
// file.
- filesnotmatched.add(new Object[] { file, protocol, type});
+ filesnotmatched.add(new Object[] { file, protocol, type });
}
}
int assocfiles = 0;
*/
for (Object[] o : filesmatched)
{
- filesnotmatched.add(new Object[] { o[0], o[1]});
+ filesnotmatched.add(new Object[] { o[0], o[1] });
}
}
}
}
for (Object[] fn : filesnotmatched)
{
- loadJalviewDataFile(fn[0], (DataSourceType) fn[1], (FileFormatI)fn[2], null);
+ loadJalviewDataFile(fn[0], (DataSourceType) fn[1],
+ (FileFormatI) fn[2], null);
}
}
}
}
alignPanel.validateAnnotationDimensions(true);
- // TODO this triggers relayout of annotation panel - otherwise annotation label height is different to panel height
+ // TODO this triggers relayout of annotation panel - otherwise annotation
+ // label height is different to panel height
alignPanel.fontChanged();
alignPanel.alignmentChanged();
}
{
return calculateIdWidth(-1, false, false);
}
+
/**
* pre 2.11.3 Id width calculation - used when importing old projects only
+ *
* @return
*/
public int getLegacyIdWidth()
{
return calculateIdWidth(maxwidth, true, false);
}
+
/**
* Calculate the width of the alignment labels based on the displayed names
* and any bounds on label width set in preferences.
*
* @param maxwidth
* -1 or maximum width allowed for IdWidth
- * @param includeAnnotations - when true includes width of any additional marks in annotation id panel
- * @param visibleOnly - when true, ignore label widths for hidden annotation rows
+ * @param includeAnnotations
+ * - when true includes width of any additional marks in annotation
+ * id panel
+ * @param visibleOnly
+ * - when true, ignore label widths for hidden annotation rows
* @return Dimension giving the maximum width of the alignment label panel
* that should be used.
*/
public Dimension calculateIdWidth(int maxwidth,
boolean includeAnnotations, boolean visibleOnly)
{
- return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations, visibleOnly);
+ return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations,
+ visibleOnly);
}
-
+
/**
* legacy mode or post 2.11.3 ID width calculation
- * @param legacy - uses annotation labels, not rendered label width (excludes additional decorators)
+ *
+ * @param legacy
+ * - uses annotation labels, not rendered label width (excludes
+ * additional decorators)
* @param maxwidth
* @param includeAnnotations
* @param visibleOnly
// this is called after loading new annotation onto alignment
if (alignFrame.getHeight() == 0)
{
- jalview.bin.Console.error("adjustAnnotationHeight called with zero height alignment window");
+ jalview.bin.Console.error(
+ "adjustAnnotationHeight called with zero height alignment window");
}
validateAnnotationDimensions(true);
addNotify();
final int idWidth, idWidthForGui;
// otherwise calculate it
idWidth = getVisibleIdWidth(false);
-// if (getIdPanel()!=null && getIdPanel().getWidth()>0)
-// {
-// // use the current IdPanel's width, if its set and non-zero
-// idWidthForGui = getIdPanel().getWidth();
-// } else {
-// idWidthForGui=0;
-// }
+ // if (getIdPanel()!=null && getIdPanel().getWidth()>0)
+ // {
+ // // use the current IdPanel's width, if its set and non-zero
+ // idWidthForGui = getIdPanel().getWidth();
+ // } else {
+ // idWidthForGui=0;
+ // }
/*
* Get the horizontal offset to where we draw the sequences.
* This is idWidth if using a single Graphics context, else zero.
final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
alignmentGraphics.setColor(Color.white);
- alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight+scaleHeight);
+ alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight + scaleHeight);
/*
* draw the Scale at horizontal offset, then reset to top left (0, 0)
IdCanvas idCanvas = getIdPanel().getIdCanvas();
List<SequenceI> selection = av.getSelectionGroup() == null ? null
: av.getSelectionGroup().getSequences(null);
-
+
idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
- selection, false,idWidth);
+ selection, false, idWidth);
idGraphics.setFont(av.getFont());
idGraphics.translate(0, -scaleHeight);
// see if rendering offscreen - check preferences and calc width accordingly
if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
{
- return calculateIdWidth(-1,true,true).width;
+ return calculateIdWidth(-1, true, true).width;
}
Integer idwidth = onscreen ? null
: Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
- this(av,ap,null);
+ this(av, ap, null);
}
- public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings)
+
+ public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,
+ AnnotationColourGradient initSettings)
{
super(av, ap);
oldcs = av.getGlobalColourScheme();
setDefaultMinMax();
adjusting = true;
- if (oldcs instanceof AnnotationColourGradient && initSettings==null)
+ if (oldcs instanceof AnnotationColourGradient && initSettings == null)
{
// init from oldcs
initialiseFrom((AnnotationColourGradient) oldcs);
- } else {
+ }
+ else
+ {
// use initial colour gradient - if any..
initialiseFrom(initSettings);
}
-
+
jbInit();
adjusting = false;
frame.invalidate();
frame.pack();
}
+
private void initialiseFrom(AnnotationColourGradient acg)
{
- if (acg!=null)
+ if (acg != null)
{
useOriginalColours.setSelected(
- acg.isPredefinedColours() || acg.getBaseColour() != null);
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
populateThresholdComboBox(threshold);
- if (acg!=null)
+ if (acg != null)
{
String label = getAnnotationMenuLabel(acg.getAnnotation());
- // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel!
+ // TODO: workaround below shouldn't be necessary - there's a bug in
+ // getAnnotationMenuLabel!
if (acg.isSeqAssociated())
{
label = acg.getAnnotation().label;
return;
}
- int selIndex = annotations
- .getSelectedIndex();
+ int selIndex = annotations.getSelectedIndex();
int annIndex = annmap[selIndex];
setCurrentAnnotation(
av.getAlignment().getAlignmentAnnotation()[annIndex]);
* @param av
* @param ap
* @param alignmentAnnotation
- * @param perseq - when true, enable per-sequence if alignment annotation is per sequence
+ * @param perseq
+ * - when true, enable per-sequence if alignment annotation is per
+ * sequence
*/
public static void displayFor(AlignViewport av, AlignmentPanel ap,
AlignmentAnnotation alignmentAnnotation, boolean perSeq)
{
ColourSchemeI global = av.getGlobalColourScheme();
- AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD);
- if (alignmentAnnotation.sequenceRef!=null)
+ AnnotationColourGradient newCS = new AnnotationColourGradient(
+ alignmentAnnotation, global,
+ alignmentAnnotation.threshold != null
+ ? AnnotationColourGradient.ABOVE_THRESHOLD
+ : AnnotationColourGradient.NO_THRESHOLD);
+ if (alignmentAnnotation.sequenceRef != null)
{
newCS.setSeqAssociated(perSeq);
}
- for (int i=0;i<alignmentAnnotation.annotations.length;i++)
+ for (int i = 0; i < alignmentAnnotation.annotations.length; i++)
{
Annotation ann = alignmentAnnotation.annotations[i];
- if (ann!=null && ann.colour!=null && !ann.colour.equals(Color.white))
+ if (ann != null && ann.colour != null
+ && !ann.colour.equals(Color.white))
{
newCS.setPredefinedColours(true);
break;
}
}
- AnnotationColourChooser achooser = new AnnotationColourChooser(av,ap,newCS);
+ AnnotationColourChooser achooser = new AnnotationColourChooser(av, ap,
+ newCS);
}
}
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
- this(av,ap,null);
+ this(av, ap, null);
}
- public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap, AlignmentAnnotation selectedAnnotation)
+
+ public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap,
+ AlignmentAnnotation selectedAnnotation)
{
super(av, ap);
frame = new JInternalFrame();
}
setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
-
+
setAnnotations(new JComboBox<>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
AnnotationColumnChooser lastChooser = av
percentThreshold
.setSelected(lastChooser.percentThreshold.isSelected());
}
- if (selectedAnnotation!=null)
+ if (selectedAnnotation != null)
{
- try {
+ try
+ {
setCurrentAnnotation(selectedAnnotation);
- annotations.setSelectedItem(getAnnotationMenuLabel(selectedAnnotation));
+ annotations.setSelectedItem(
+ getAnnotationMenuLabel(selectedAnnotation));
} catch (Exception x)
{
- Console.error("Couldn't select annotation in column chooser",x);
+ Console.error("Couldn't select annotation in column chooser", x);
}
}
public static void displayFor(AlignViewport av, AlignmentPanel ap,
AlignmentAnnotation alignmentAnnotation)
{
- AnnotationColumnChooser colchooser = new AnnotationColumnChooser(av, ap, alignmentAnnotation);
+ AnnotationColumnChooser colchooser = new AnnotationColumnChooser(av, ap,
+ alignmentAnnotation);
}
}
* @param width
* Width for scaling labels
*/
- public void drawComponent(Graphics g, boolean clip, int givenWidth, boolean forGUI)
+ public void drawComponent(Graphics g, boolean clip, int givenWidth,
+ boolean forGUI)
{
int width = givenWidth;
IdwidthAdjuster iwa = null;
{
Graphics2D g2d = (Graphics2D) g;
Graphics dummy = g2d.create();
- int newAnnotationIdWidth = drawLabels(dummy, clip, width, false, forGUI,
- null, false);
+ int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+ forGUI, null, false);
dummy.dispose();
Dimension d = ap.calculateDefaultAlignmentIdWidth();
int alignmentIdWidth = d.width;
}
else
{
- int newAnnotationIdWidth = drawLabels(g, clip, width, false, forGUI, null, false);
- width = newAnnotationIdWidth<givenWidth ? givenWidth: Math.min(newAnnotationIdWidth, givenWidth);
+ int newAnnotationIdWidth = drawLabels(g, clip, width, false, forGUI,
+ null, false);
+ width = newAnnotationIdWidth < givenWidth ? givenWidth
+ : Math.min(newAnnotationIdWidth, givenWidth);
}
drawLabels(g, clip, width, true, forGUI, null, false);
}
* fmetrics must be supplied.
*
* @param g
- * Graphics2D instance (used for rendering and font scaling if no fmetrics supplied)
+ * Graphics2D instance (used for rendering and font scaling if no
+ * fmetrics supplied)
* @param clip
* - true indicates that only current visible area needs to be
* rendered
* @param width
* Width for scaling labels
- * @param actuallyDraw - when false, no graphics are rendered to g0
- * @param forGUI - when false, GUI relevant marks like indicators for dragging annotation panel height are not rendered
+ * @param actuallyDraw
+ * - when false, no graphics are rendered to g0
+ * @param forGUI
+ * - when false, GUI relevant marks like indicators for dragging
+ * annotation panel height are not rendered
* @param fmetrics
* FontMetrics if Graphics object g is null
- * @param includeHidden - when true returned width includes labels in hidden row width calculation
+ * @param includeHidden
+ * - when true returned width includes labels in hidden row width
+ * calculation
* @return the width of the annotation labels.
*/
public int drawLabels(Graphics g0, boolean clip, int width,
- boolean actuallyDraw, boolean forGUI, FontMetrics fmetrics, boolean includeHidden)
+ boolean actuallyDraw, boolean forGUI, FontMetrics fmetrics,
+ boolean includeHidden)
{
if (clip)
{
}
}
- if (!resizePanel && dragEvent != null && aa != null && selectedRow>-1 && selectedRow<aa.length)
+ if (!resizePanel && dragEvent != null && aa != null && selectedRow > -1
+ && selectedRow < aa.length)
{
if (actuallyDraw && g != null)
{
int yOffset = rowIndex[1];
AlignmentAnnotation[] allAnnotation = av.getAlignment()
.getAlignmentAnnotation();
- if (allAnnotation==null || rowIndex[0]<0 || rowIndex[0]>=allAnnotation.length)
+ if (allAnnotation == null || rowIndex[0] < 0
+ || rowIndex[0] >= allAnnotation.length)
{
return false;
}
if (forFromX != null && forToX != null)
{
- // FIXME will need two ContactGeometry objects when handling contact matrices with differing numbers of rows at each
+ // FIXME will need two ContactGeometry objects when handling contact
+ // matrices with differing numbers of rows at each
// column
ContactGeometry xcgeom = new ContactGeometry(forFromX,
cma.graphHeight);
- ContactGeometry.contactInterval lastXci = xcgeom
- .mapFor(rowIndex[1]);
- ContactGeometry.contactInterval cXci = xcgeom.mapFor(rowIndex[1] + deltaY);
+ ContactGeometry.contactInterval lastXci = xcgeom.mapFor(rowIndex[1]);
+ ContactGeometry.contactInterval cXci = xcgeom
+ .mapFor(rowIndex[1] + deltaY);
// mark rectangular region formed by drag
jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
// }
// else
{
- av.getColumnSelection().addElement(c-1);
+ av.getColumnSelection().addElement(c - 1);
}
}
}
{
row = i;
res[0] = row;
- res[1] = yPos-lheight;
+ res[1] = yPos - lheight;
break;
}
}
// TODO abstract tooltip generator so different implementations can be built
if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
{
- if (rowAndOffset>=ann.graphHeight)
+ if (rowAndOffset >= ann.graphHeight)
{
return null;
}
ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
StringBuilder tooltipb = new StringBuilder();
- tooltipb.append("Contact from ")
- .append(clist.getPosition()).append(", [").append(ci.cStart).append(" - ").append(ci.cEnd).append("]").append("<br/>Mean:");
- Format.appendPercentage(tooltipb, (float)cr.getMean(),2);
+ tooltipb.append("Contact from ").append(clist.getPosition())
+ .append(", [").append(ci.cStart).append(" - ")
+ .append(ci.cEnd).append("]").append("<br/>Mean:");
+ Format.appendPercentage(tooltipb, (float) cr.getMean(), 2);
tooltip = tooltipb.toString();
int col = ann.sequenceRef.findPosition(column);
int[][] highlightPos;
&& (fadedImage == null || fadedImage.getWidth() != imgWidth
|| fadedImage.getHeight() != image.getHeight()))
{
- // jalview.bin.Console.errPrintln("redraw faded image ("+(fadedImage==null ?
+ // jalview.bin.Console.errPrintln("redraw faded image
+ // ("+(fadedImage==null ?
// "null image" : "") + " lastGood="+lastImageGood+")");
fadedImage = new BufferedImage(imgWidth, image.getHeight(),
BufferedImage.TYPE_INT_RGB);
if (shift != null)
{
int i = shift.shift(newBase.getIndex());
- // jalview.bin.Console.errPrintln("shifted "+(arg1.getIndex())+" to "+i);
+ // jalview.bin.Console.errPrintln("shifted "+(arg1.getIndex())+" to
+ // "+i);
ssm.mouseOverVamsasSequence(seq, i, this);
}
else
} catch (ExceptionNAViewAlgorithm e)
{
// only throwable for draw mode = 3 NAView
- jalview.bin.Console.errPrintln("Error drawing RNA: " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error drawing RNA: " + e.getMessage());
}
}
}
boolean opened = jmb.openSession(chimeraSessionFile);
if (!opened)
{
- jalview.bin.Console.errPrintln("An error occurred opening Chimera session file "
- + chimeraSessionFile);
+ jalview.bin.Console.errPrintln(
+ "An error occurred opening Chimera session file "
+ + chimeraSessionFile);
}
}
}
} catch (Exception ex)
{
- jalview.bin.Console.outPrintln("Error loading User ColourFile\n" + ex);
+ jalview.bin.Console
+ .outPrintln("Error loading User ColourFile\n" + ex);
}
}
// logLevelCombo.addItem(LogLevel.ERROR);
// logLevelCombo.addItem(LogLevel.OFF);
// set startingLogLevel
-
+
if (jalview.bin.Console.getLogger() == null)
{
startingLogLevel = jalview.bin.Console.getCachedLogLevel();
@Override
public void run()
{
- displayPipe.append(input);
+ displayPipe.append(input);
}
});
// stderr.println("Time taken to Spawnappend:\t" + (System.nanoTime() -
if (copyAlignment.getHeight() <= 0)
{
- jalview.bin.Console.errPrintln("No Sequences generated for xRef type " + source);
+ jalview.bin.Console
+ .errPrintln("No Sequences generated for xRef type " + source);
return null;
}
*/
final String ft = features.get(featureIndex).getType();
final String type = ft == null ? lastFeatureAdded : ft;
- FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type,true);
+ FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type, true);
fcc.setRequestFocusEnabled(true);
fcc.requestFocus();
fcc.addActionListener(new ActionListener()
*/
String ttl = MessageManager
.formatMessage("label.select_colour_for", type);
- Object last=(Boolean)table.getValueAt(selectedRow, SHOW_COLUMN);
+ Object last = (Boolean) table.getValueAt(selectedRow,
+ SHOW_COLUMN);
table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN);
ColourChooserListener listener = new ColourChooserListener()
{
/*
* variable colour and filters dialog
*/
- boolean last=(Boolean)table.getValueAt(selectedRow, SHOW_COLUMN);
+ boolean last = (Boolean) table.getValueAt(selectedRow,
+ SHOW_COLUMN);
table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN);
- chooser = new FeatureTypeSettings(fr, type,last);
+ chooser = new FeatureTypeSettings(fr, type, last);
if (!Platform.isJS())
/**
* Java only
if (button == e.getSource())
{
boolean last = fr.getFeaturesDisplayed().isVisible(type);
- ((FeatureTableModel) table.getModel()).setValueAt(Boolean.TRUE, rowSelected, SHOW_COLUMN);
- FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type,last);
+ ((FeatureTableModel) table.getModel()).setValueAt(Boolean.TRUE,
+ rowSelected, SHOW_COLUMN);
+ FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type,
+ last);
chooser.addActionListener(this);
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
data[COLOUR_COLUMN] = currentColor;
data[FILTER_COLUMN] = currentFilter;
data[SHOW_COLUMN] = fr.getFeaturesDisplayed().isVisible(type);
-
+
fireEditingStopped();
// SwingJS needs an explicit repaint() here,
// rather than relying upon no validation having
refreshDisplay();
}
}
+
class FeatureIcon implements Icon
{
FeatureColourI gcol;
*
* @param frender
* @param theType
- * @param last - visibility of feature prior to adjustment
+ * @param last
+ * - visibility of feature prior to adjustment
*/
- public FeatureTypeSettings(FeatureRenderer frender, String theType, boolean last)
+ public FeatureTypeSettings(FeatureRenderer frender, String theType,
+ boolean last)
{
this.fr = frender;
this.featureType = theType;
{
fr.setColour(featureType, originalColour);
fr.setFeatureFilter(featureType, originalFilter);
- if (!originalDisplay) {
+ if (!originalDisplay)
+ {
fr.getFeaturesDisplayed().setHidden(featureType);
}
refreshDisplay(true);
gg.fillRect(0, 0, getWidth(), imgHeight);
drawIds(gg, av, av.getRanges().getStartSeq(),
- av.getRanges().getEndSeq(), searchResults,true, getWidth());
+ av.getRanges().getEndSeq(), searchResults, true, getWidth());
gg.dispose();
* @param startSeq
* @param endSeq
* @param selection
- * @param forGUI when false rendering for print
- * @param panelWidth width used to calculate righthand margin - usually idCanvas.getWidth()
+ * @param forGUI
+ * when false rendering for print
+ * @param panelWidth
+ * width used to calculate righthand margin - usually
+ * idCanvas.getWidth()
*
*/
void drawIds(Graphics2D g, AlignViewport alignViewport,
- final int startSeq, final int endSeq, List<SequenceI> selection, boolean forGUI, int panelWidth)
+ final int startSeq, final int endSeq, List<SequenceI> selection,
+ boolean forGUI, int panelWidth)
{
Font font = alignViewport.getFont();
if (alignViewport.isSeqNameItalics())
if (alignViewport.getWrapAlignment())
{
- drawIdsWrapped(g, alignViewport, startSeq, getHeight(), manuallyAdjusted ? panelWidth : -1,forGUI);
+ drawIdsWrapped(g, alignViewport, startSeq, getHeight(),
+ manuallyAdjusted ? panelWidth : -1, forGUI);
return;
}
/**
* render sequence IDs and annotation labels when wrapped - without GUI junk
+ *
* @param g
* @param av2
* @param i
public void drawIdsWrappedNoGUI(Graphics2D g, AlignViewport av2, int i,
int totalHeight)
{
- drawIdsWrapped(g, av2, totalHeight, totalHeight, i,false);
+ drawIdsWrapped(g, av2, totalHeight, totalHeight, i, false);
}
public void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
if (alignViewport.isShowAnnotation())
{
// in wrapped mode, no alignPanel reference is available
- // FIXME: make the renderer not create a new object in wrapped mode everytime!
+ // FIXME: make the renderer not create a new object in wrapped mode
+ // everytime!
labels = new AnnotationLabels(alignViewport);
}
g.translate(0, ypos + (alheight * charHeight));
if (!isManuallyAdjusted())
{
- int getAnnotationsIdWidth = labels.drawLabels(g, false, -1, false,forGUI,
- null, false);
+ int getAnnotationsIdWidth = labels.drawLabels(g, false, -1, false,
+ forGUI, null, false);
thisIdWidth = idWidth < 0 ? getAnnotationsIdWidth : idWidth;
if (thisIdWidth > getWidth)
{
{
return;
}
-
+
// TODO JAL-4260 - work out how to trigger recomputation of wrapped pages !
int curCol = viewport.getRanges().getStartRes()
+ viewport.getRanges().getViewportWidth();
-
+
viewport.setIdWidth(newWidth);
ap.validateAnnotationDimensions(false);
curCol - viewport.getRanges().getViewportWidth());
}
ap.paintAlignment(true, false);
-
+
ap.getIdPanel().getIdCanvas().setManuallyAdjusted(true);
}
};
String pca = MessageManager.getString("label.pca");
ImageExporter exporter = new ImageExporter(writer, null, type, pca);
- try {
+ try
+ {
exporter.doExport(null, this, width, height, pca);
- } catch (ImageOutputException ioex) {
- Console.error("Unexpected error whilst writing "+type.toString(),ioex);
+ } catch (ImageOutputException ioex)
+ {
+ Console.error("Unexpected error whilst writing " + type.toString(),
+ ioex);
}
}
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
final AlignmentI alignment = this.ap.getAlignment();
- AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- null);
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
refresh();
}
String[] omitHidden = null;
- jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a
+ // prompt happens
// or we simply trust the user wants
// wysiwig behaviour
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[]
}
av.setSelectionGroup(sg);
ap.paintAlignment(false, false);
- PaintRefresher.Refresh(this,av.getSequenceSetId());
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
av.sendSelection();
}
ap.getSeqPanel().stopScrolling();
int res = ap.getSeqPanel().findAlignmentColumn(evt);
-
+
if (!stretchingGroup)
{
if (evt.isPopupTrigger()) // Windows: mouseReleased
@Override
public void mouseDragged(MouseEvent evt)
{
- mouseDragging = true;
+ mouseDragging = true;
int res = ap.getSeqPanel().findAlignmentColumn(evt);
-
+
ColumnSelection cs = av.getColumnSelection();
-
- min = Math.min(res,min);
+
+ min = Math.min(res, min);
max = Math.max(res, max);
SequenceGroup sg = av.getSelectionGroup();
this.setToolTipText(null);
reveal = null;
final int res = ap.getSeqPanel().findAlignmentColumn(evt);
-
+
highlightAllStructPos(res);
- if (!av.hasHiddenColumns()) {
+ if (!av.hasHiddenColumns())
+ {
return;
}
reveal = av.getAlignment().getHiddenColumns()
- .getRegionWithEdgeAtRes(av.getAlignment().getHiddenColumns().absoluteToVisibleColumn(res));
- if (reveal==null)
+ .getRegionWithEdgeAtRes(av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(res));
+ if (reveal == null)
{
return;
}
// group
if (sx >= 0 && sx < visWidth)
{
- g.drawLine(sx, oldY, sx, sy-1);
+ g.drawLine(sx, oldY, sx, sy - 1);
}
// if end position is visible, draw vertical line to right of
// group
if (sx + xwidth < visWidth)
{
- g.drawLine(sx + xwidth, oldY, sx + xwidth, sy-1);
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy - 1);
}
}
*/
int findAlignmentColumn(MouseEvent evt)
{
- return findNearestColumn(evt,true);
+ return findNearestColumn(evt, true);
}
+
/**
* Returns the aligned sequence position (base 0) at the mouse position, or
* the closest visible one
{
return findNearestColumn(evt, false);
}
-
+
/**
- * @param nearestColumn when false returns negative values for out of bound positions - -1 for scale left/right, <-1 if far to right
+ * @param nearestColumn
+ * when false returns negative values for out of bound positions - -1
+ * for scale left/right, <-1 if far to right
* @return nearest absolute column to mouse pointer
*/
private int findNearestColumn(MouseEvent evt, boolean nearestColumn)
if (x < 0)
{
// mouse is over left scale
- if (!nearestColumn) {
+ if (!nearestColumn)
+ {
return -1;
- } else {
+ }
+ else
+ {
x = 0;
}
}
}
if (x >= cwidth * charWidth)
{
- if (!nearestColumn) {
+ if (!nearestColumn)
+ {
// mouse is over right scale
return -1;
- } else {
- x = cwidth*charWidth -1;
+ }
+ else
+ {
+ x = cwidth * charWidth - 1;
}
}
res = Math.min(res, av.getRanges().getEndRes());
}
-
if (av.hasHiddenColumns())
{
List<SequenceI> seqsWithoutSourceDBRef = null;
private boolean showChooserGUI = true;
+
/**
- * when true, queries to external services are supressed (no SIFTs, no PDBe, no 3D-Beacons, etc)
+ * when true, queries to external services are supressed (no SIFTs, no PDBe,
+ * no 3D-Beacons, etc)
*/
private boolean dontQueryServices = false;
{
this(selectedSeqs, selectedSeq, ap, showGUI, false);
}
-
+
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap, boolean showGUI, boolean dontQueryServices)
{
}
}).start();
- } else {
- Console.debug("Structure chooser not querying services to discover metadata.");
+ }
+ else
+ {
+ Console.debug(
+ "Structure chooser not querying services to discover metadata.");
}
}
.getFTSDataFor(getResultTable(), selectedRow,
discoveredStructuresSet);
String pageUrl = row.getModelViewUrl();
-
+
JPopupMenu popup = new JPopupMenu("3D Beacons");
JMenuItem viewUrl = new JMenuItem("View model web page");
- if (pageUrl == null || "".equals(pageUrl.trim())) {
+ if (pageUrl == null || "".equals(pageUrl.trim()))
+ {
viewUrl.setEnabled(false);
viewUrl.setText("No model page available.");
}
// headless = true;
prompt = false;
// suppress structure viewer's external service queries
- sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,true);
+ sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,
+ true);
}
if (ssm == null)
{
}
/**
- * Singleton list of all (open) instances of structureViewerBase
- * TODO: JAL-3362 - review and adopt the swingJS-safe singleton pattern so each structure viewer base instance is kept to its own JalviewJS parent
+ * Singleton list of all (open) instances of structureViewerBase TODO:
+ * JAL-3362 - review and adopt the swingJS-safe singleton pattern so each
+ * structure viewer base instance is kept to its own JalviewJS parent
*/
private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
chainMenu.add(menuItem);
}
}
- void setHetatmMenuItems(Map<String,String> hetatmNames)
+
+ void setHetatmMenuItems(Map<String, String> hetatmNames)
{
hetatmMenu.removeAll();
if (hetatmNames == null || hetatmNames.isEmpty())
return;
}
hetatmMenu.setVisible(true);
- allHetatmBeingSelected=false;
+ allHetatmBeingSelected = false;
JMenuItem allMenuItem = new JMenuItem(
MessageManager.getString("label.all"));
JMenuItem noneMenuItem = new JMenuItem(
allMenuItem.addActionListener(new ActionListener()
{
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
{
- allHetatmBeingSelected=true;
- // Toggle state of everything - on
- for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
- if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ allHetatmBeingSelected = true;
+ // Toggle state of everything - on
+ for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
- ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+ if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+ }
}
+ allHetatmBeingSelected = false;
+ showSelectedHetatms();
}
- allHetatmBeingSelected=false;
- showSelectedHetatms();
}
- }});
+ });
noneMenuItem.addActionListener(new ActionListener()
{
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
{
- allHetatmBeingSelected=true;
- // Toggle state of everything off
- for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
- if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ allHetatmBeingSelected = true;
+ // Toggle state of everything off
+ for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
- ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(false);
+ if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) hetatmMenu.getItem(i))
+ .setSelected(false);
+ }
}
+ allHetatmBeingSelected = false;
+ showSelectedHetatms();
}
- allHetatmBeingSelected=false;
- showSelectedHetatms();
}
- }});
+ });
hetatmMenu.add(noneMenuItem);
hetatmMenu.add(allMenuItem);
for (Map.Entry<String, String> chain : hetatmNames.entrySet())
{
- JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(), false);
+ JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(),
+ false);
menuItem.setToolTipText(chain.getValue());
menuItem.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent evt)
{
if (!allHetatmBeingSelected)
- {
+ {
// update viewer only when we were clicked, not programmatically
// checked/unchecked
showSelectedHetatms();
}
getBinding().showChains(toshow);
}
+
/**
* Display selected hetatms in viewer
*/
}
getBinding().showHetatms(toshow);
}
+
/**
* Tries to fetch a PDB file and save to a temporary local file. Returns the
* saved file path if successful, or null if not.
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
// jmb = null;
-
- try {
+
+ try
+ {
svbs.remove(this);
} catch (Throwable t)
{
- Console.info("Unexpected exception when deregistering structure viewer",t);
+ Console.info(
+ "Unexpected exception when deregistering structure viewer",
+ t);
}
dispose();
}
scrollPane = scroller;
addMouseListener(this);
addMouseMotionListener(this);
-
+
ToolTipManager.sharedInstance().registerComponent(this);
}
PaintRefresher.Refresh(tp, av.getSequenceSetId());
repaint();
}
+
/**
* DOCUMENT ME!
*
longestName = "";
AlignmentAnnotation aa = tp.getAssocAnnotation();
- ContactMatrixI cm = (aa!=null) ? av.getContactMatrix(aa) : null;
- if (cm!=null && cm.hasCutHeight())
+ ContactMatrixI cm = (aa != null) ? av.getContactMatrix(aa) : null;
+ if (cm != null && cm.hasCutHeight())
{
- threshold=(float) cm.getCutHeight();
+ threshold = (float) cm.getCutHeight();
}
-
+
for (int i = 0; i < leaves.size(); i++)
{
BinaryNode lf = leaves.elementAt(i);
longestName = TreeCanvas.PLACEHOLDER
+ ((Sequence) lf.element()).getName();
}
- if (tp.isColumnWise() && cm!=null)
+ if (tp.isColumnWise() && cm != null)
{
// get color from group colours, if they are set for the matrix
- try {
+ try
+ {
Color col = cm.getGroupColorForPosition(parseColumnNode(lf));
- setColor(lf,col.brighter());
- } catch (NumberFormatException ex) {};
+ setColor(lf, col.brighter());
+ } catch (NumberFormatException ex)
+ {
+ }
+ ;
}
}
if (top.count == 0)
{
- top.count = top.left().count
- + top.right().count;
+ top.count = top.left().count + top.right().count;
}
float chunk = (float) (height - (offy)) / top.count;
Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
if (tp.isColumnWise())
{
- markColumnsFor(getAssociatedPanels(), leaves, Color.red,false);
+ markColumnsFor(getAssociatedPanels(), leaves, Color.red, false);
}
else
{
for (int i = 0; i < groups.size(); i++)
{
Color col = ColorUtils.getARandomColor();
-
+
setColor(groups.get(i), col.brighter());
Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
}
}
}
+
private int parseColumnNode(BinaryNode bn) throws NumberFormatException
{
return Integer.parseInt(
bn.getName().substring(bn.getName().indexOf("c") + 1));
}
+
private boolean isColumnForNodeSelected(BinaryNode bn)
{
SequenceI rseq = tp.assocAnnotation.sequenceRef;
ColumnSelection cs = av.getColumnSelection();
HiddenColumns hc = av.getAlignment().getHiddenColumns();
AlignmentAnnotation aa = tp.getAssocAnnotation();
- int offp=-1;
+ int offp = -1;
if (aa != null)
{
ContactMatrixI cm = av.getContactMatrix(aa);
- // generally, we assume cm has 1:1 mapping to annotation row - probably wrong
+ // generally, we assume cm has 1:1 mapping to annotation row - probably
+ // wrong
// but.. if
if (cm instanceof MappableContactMatrixI)
{
int[] pos;
- // use the mappable's mapping - always the case for PAE Matrices so good
+ // use the mappable's mapping - always the case for PAE Matrices so good
// for 2.11.3
MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
pos = mcm.getMappedPositionsFor(rseq, colm + 1);
{
offp = rseq.findIndex(pos[0]);
}
- } else {
+ }
+ else
+ {
offp = colm;
}
}
- if (offp<=0)
+ if (offp <= 0)
{
return false;
}
- offp-=2;
+ offp -= 2;
if (!av.hasHiddenColumns())
{
return cs.contains(offp);
}
return false;
}
+
private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
{
BitSet gp = new BitSet();
{
continue;
}
- if (mcm!=null)
+ if (mcm != null)
{
- int[] seqpos = mcm.getMappedPositionsFor(
- rseq, colm);
+ int[] seqpos = mcm.getMappedPositionsFor(rseq, colm);
if (seqpos == null)
{
// no mapping for this column.
continue;
}
// TODO: handle ranges...
- offp = rseq.findIndex(seqpos[0])-1;
+ offp = rseq.findIndex(seqpos[0]) - 1;
}
else
{
treeCanvas = new TreeCanvas(this, ap, scrollPane);
scrollPane.setViewportView(treeCanvas);
-
+
if (columnWise)
{
bootstrapMenu.setVisible(false);
sortAssocViews.setVisible(false);
}
-
addKeyListener(new KeyAdapter()
{
@Override
public void keyPressed(KeyEvent e)
{
switch (e.getKeyCode())
- {
+ {
case 27: // escape
treeCanvas.clearSelectedLeaves();
e.consume();
break;
-
+
}
-
+
}
});
PaintRefresher.Register(this, ap.av.getSequenceSetId());
? new NJTree(av, sm, similarityParams)
: new AverageDistanceTree(av, sm, similarityParams);
tree = new TreeModel(njtree);
- // don't display distances for columnwise trees
+ // don't display distances for columnwise trees
}
showDistances(!columnWise);
tree.reCount(tree.getTopNode());
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
- try {
- exporter.doExport(null, this, width, height,
- tree.toLowerCase(Locale.ROOT));
- } catch (ImageOutputException ioex) {
- Console.error("Unexpected error whilst writing "+imageFormat.toString(),ioex);
+ try
+ {
+ exporter.doExport(null, this, width, height,
+ tree.toLowerCase(Locale.ROOT));
+ } catch (ImageOutputException ioex)
+ {
+ Console.error(
+ "Unexpected error whilst writing " + imageFormat.toString(),
+ ioex);
}
}
// we only care about AlignmentSequence selections
SelectionMessage sm = (SelectionMessage) message;
sm.validate();
- jalview.bin.Console.errPrintln("Received\n" + sm.getRawMessage());
+ jalview.bin.Console
+ .errPrintln("Received\n" + sm.getRawMessage());
Object[] jvobjs = sm.getVorbaIDs() == null ? null
: new Object[sm.getVorbaIDs().length];
if (jvobjs == null)
}
else
{
- jalview.bin.Console.errPrintln("Ignoring unknown service argument type "
- + myarg.getClass().getName());
+ jalview.bin.Console
+ .errPrintln("Ignoring unknown service argument type "
+ + myarg.getClass().getName());
}
}
}
disc.run();
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Aborting. Problem discovering services.");
+ jalview.bin.Console
+ .errPrintln("Aborting. Problem discovering services.");
e.printStackTrace();
return;
}
Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
+ jalview.bin.Console
+ .errPrintln("Failed to copy " + o.getName());
e.printStackTrace();
} catch (Error e)
{
- jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
+ jalview.bin.Console
+ .errPrintln("Failed to copy " + o.getName());
e.printStackTrace();
}
}
.copyParameter(o);
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
+ jalview.bin.Console
+ .errPrintln("Failed to copy " + o.getName());
e.printStackTrace();
} catch (Error e)
{
- jalview.bin.Console.errPrintln("Failed to copy " + o.getName());
+ jalview.bin.Console
+ .errPrintln("Failed to copy " + o.getName());
e.printStackTrace();
}
}
return;
}
curSetName = newname;
- jalview.bin.Console.errPrintln("New name for user setting " + curSetName
- + " (was " + setName.getSelectedItem() + ")");
+ jalview.bin.Console.errPrintln("New name for user setting "
+ + curSetName + " (was " + setName.getSelectedItem() + ")");
if (curSetName.equals(setName.getSelectedItem()))
{
curSetName = null;
}
else
{
- // jalview.bin.Console.errPrintln("Skipping NaN - not valid value.");
+ // jalview.bin.Console.errPrintln("Skipping NaN - not valid
+ // value.");
text.append(comma + 0f);// row.annotations[j].value);
}
comma = ",";
} catch (Exception ex)
{
ex.printStackTrace();
- jalview.bin.Console.outPrintln("Problem reading annotation file: " + ex);
+ jalview.bin.Console
+ .outPrintln("Problem reading annotation file: " + ex);
if (nlinesread > 0)
{
- jalview.bin.Console.outPrintln("Last read line " + nlinesread + ": '" + lastread
- + "' (first 80 chars) ...");
+ jalview.bin.Console.outPrintln("Last read line " + nlinesread
+ + ": '" + lastread + "' (first 80 chars) ...");
}
return false;
}
value = Float.valueOf(nextToken);
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln("line " + nlinesread + ": Threshold '" + nextToken
- + "' invalid, setting to zero");
+ jalview.bin.Console.errPrintln("line " + nlinesread + ": Threshold '"
+ + nextToken + "' invalid, setting to zero");
}
String label = st.hasMoreTokens() ? st.nextToken() : null;
Color colour = null;
} catch (Exception e)
{
e.printStackTrace();
- jalview.bin.Console.errPrintln("Failed to read alignment using the '" + fileFormat
- + "' reader.\n" + e);
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+ + fileFormat + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
} catch (Exception e)
{
e.printStackTrace();
- jalview.bin.Console.errPrintln("Failed to read alignment using the '" + format
- + "' reader.\n" + e);
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+ + format + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
- jalview.bin.Console.errPrintln("Warning raised when writing as " + format
- + " : " + afile.getWarningMessage());
+ jalview.bin.Console.errPrintln("Warning raised when writing as "
+ + format + " : " + afile.getWarningMessage());
}
return afileresp;
} catch (Exception e)
memf += r.totalMemory() - r.freeMemory();
if (al != null)
{
- jalview.bin.Console.outPrintln("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
+ jalview.bin.Console.outPrintln("Alignment contains "
+ + al.getHeight() + " sequences and " + al.getWidth()
+ + " columns.");
try
{
jalview.bin.Console.outPrintln(new AppletFormatAdapter()
{
jalview.bin.Console.outPrintln("Couldn't read alignment");
}
- jalview.bin.Console.outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
+ jalview.bin.Console
+ .outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
jalview.bin.Console.outPrintln(
"Difference between free memory now and before is "
+ (memf / (1024.0 * 1024.0) * 1.0) + " MB");
}
else
{
- jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] + "' (" + i
- + "'th)- not a readable file.");
+ jalview.bin.Console.errPrintln("Ignoring argument '" + args[i]
+ + "' (" + i + "'th)- not a readable file.");
}
i++;
}
DataSourceType protocol = null;
if (debug)
{
- jalview.bin.Console.outPrintln("resolving datasource started with:\n>>file\n"
- + file + ">>endfile");
+ jalview.bin.Console
+ .outPrintln("resolving datasource started with:\n>>file\n"
+ + file + ">>endfile");
}
// This might throw a security exception in certain browsers
{
if (debug)
{
- jalview.bin.Console.errPrintln("Exception when accessing content: " + e);
+ jalview.bin.Console
+ .errPrintln("Exception when accessing content: " + e);
}
fp = null;
}
}
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Failed to access content as paste!");
+ jalview.bin.Console
+ .errPrintln("Failed to access content as paste!");
e.printStackTrace();
fp = null;
}
{
if (debug)
{
- jalview.bin.Console.outPrintln("Format not identified. Inaccessible file.");
+ jalview.bin.Console.outPrintln(
+ "Format not identified. Inaccessible file.");
}
return null;
}
{
if (debug)
{
- jalview.bin.Console.outPrintln("Protocol identified as " + protocol);
+ jalview.bin.Console
+ .outPrintln("Protocol identified as " + protocol);
}
return protocol;
}
{
if (debug)
{
- jalview.bin.Console.errPrintln("File deemed not accessible via " + protocol);
+ jalview.bin.Console
+ .errPrintln("File deemed not accessible via " + protocol);
e.printStackTrace();
}
}
}
} catch (IOException e)
{
- jalview.bin.Console.outPrintln("IOException when checking file '" + filename
- + "' is a backupfile");
+ jalview.bin.Console.outPrintln("IOException when checking file '"
+ + filename + "' is a backupfile");
}
BackupFilenameParts bffp = new BackupFilenameParts(filename, base,
{
if (!biojsDirectory.mkdirs())
{
- jalview.bin.Console.outPrintln("Couldn't create local directory : "
- + BJS_TEMPLATES_LOCAL_DIRECTORY);
+ jalview.bin.Console
+ .outPrintln("Couldn't create local directory : "
+ + BJS_TEMPLATES_LOCAL_DIRECTORY);
return;
}
}
} catch (OutOfMemoryError err)
{
- jalview.bin.Console.outPrintln("########################\n" + "OUT OF MEMORY "
- + generatedFile + "\n" + "########################");
+ jalview.bin.Console
+ .outPrintln("########################\n" + "OUT OF MEMORY "
+ + generatedFile + "\n" + "########################");
new OOMWarning("Creating Image for " + generatedFile, err);
} catch (Exception e)
{
}
else
{
- jalview.bin.Console.errPrintln("Clustal File Reader: Can't find sequence for "
- + headers.elementAt(i));
+ jalview.bin.Console.errPrintln(
+ "Clustal File Reader: Can't find sequence for "
+ + headers.elementAt(i));
}
}
AlignmentAnnotation lastssa = null;
// should report somewhere useful for UI if necessary
warningMessage = ((warningMessage == null) ? "" : warningMessage)
+ "Parsing error at\n" + line;
- jalview.bin.Console.outPrintln("Error parsing feature file: " + ex + "\n" + line);
+ jalview.bin.Console.outPrintln(
+ "Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
return false;
String[] tokens = line.split(TAB_REGEX);
if (tokens.length != 2)
{
- jalview.bin.Console.errPrintln(String.format("Invalid token count %d for %d",
- tokens.length, line));
+ jalview.bin.Console.errPrintln(String.format(
+ "Invalid token count %d for %d", tokens.length, line));
}
else
{
seq = alignment.getSequenceAt(idx);
} catch (NumberFormatException ex)
{
- jalview.bin.Console.errPrintln("Invalid sequence index: " + seqIndex);
+ jalview.bin.Console
+ .errPrintln("Invalid sequence index: " + seqIndex);
}
}
@Override
public String print(SequenceI[] sqs, boolean jvsuffix)
{
- jalview.bin.Console.outPrintln("Use printGffFormat() or printJalviewFormat()");
+ jalview.bin.Console
+ .outPrintln("Use printGffFormat() or printJalviewFormat()");
return null;
}
*/
if (gffColumns.length < 5)
{
- jalview.bin.Console.errPrintln("Ignoring GFF feature line with too few columns ("
- + gffColumns.length + ")");
+ jalview.bin.Console
+ .errPrintln("Ignoring GFF feature line with too few columns ("
+ + gffColumns.length + ")");
return null;
}
}
} catch (IOException e)
{
- jalview.bin.Console.errPrintln("GFF parsing failed with: " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("GFF parsing failed with: " + e.getMessage());
return null;
}
}
return new FeaturesFile();
}
},
- FeatureSettings("Jalview Feature Settings File","fc",false,false)
+ FeatureSettings("Jalview Feature Settings File", "fc", false, false)
{
@Override
public AlignmentFileReaderI getReader(FileParse source)
public AlignmentFileWriterI getWriter(AlignmentI al)
{
return null;
- }
+ }
},
ScoreMatrix("Substitution matrix", "", false, false)
{
String name = format.getName().toUpperCase(Locale.ROOT);
if (formats.containsKey(name))
{
- jalview.bin.Console.errPrintln("Overwriting file format: " + format.getName());
+ jalview.bin.Console
+ .errPrintln("Overwriting file format: " + format.getName());
}
formats.put(name, format);
if (isIdentifiable)
exportHTML(outputFile, null);
}
- public void exportHTML(String outputFile, String renderer) throws ImageOutputException
+ public void exportHTML(String outputFile, String renderer)
+ throws ImageOutputException
{
setProgressMessage(MessageManager.formatMessage(
"status.exporting_alignment_as_x_file", getDescription()));
}
} catch (OutOfMemoryError err)
{
- jalview.bin.Console.outPrintln("########################\n" + "OUT OF MEMORY "
- + generatedFile + "\n" + "########################");
+ jalview.bin.Console
+ .outPrintln("########################\n" + "OUT OF MEMORY "
+ + generatedFile + "\n" + "########################");
new OOMWarning("Creating Image for " + generatedFile, err);
} catch (Exception e)
{
reply = FileFormat.Rnaml;
break;
}
- if (isXml && data.contains("<NS2:JALVIEWUSERCOLOURS SCHEMENAME=\"SEQUENCE FEATURES\" XMLNS:NS2=\"WWW.JALVIEW.ORG/COLOURS\">"))
+ if (isXml && data.contains(
+ "<NS2:JALVIEWUSERCOLOURS SCHEMENAME=\"SEQUENCE FEATURES\" XMLNS:NS2=\"WWW.JALVIEW.ORG/COLOURS\">"))
{
reply = FileFormat.FeatureSettings;
break;
for (int i = 0; i < jpred.seqs.size(); i++)
{
- jalview.bin.Console.outPrintln(((Sequence) jpred.seqs.elementAt(i)).getName()
- + "\n"
- + ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString()
- + "\n");
+ jalview.bin.Console
+ .outPrintln(((Sequence) jpred.seqs.elementAt(i)).getName()
+ + "\n" + ((Sequence) jpred.seqs.elementAt(i))
+ .getSequenceAsString()
+ + "\n");
}
} catch (java.io.IOException e)
{
.setSecondaryStructure(annotation.secondaryStructure);
String displayChar = annotation.displayCharacter == null ? null
: annotation.displayCharacter;
- // jalview.bin.Console.outPrintln("--------------------->[" + displayChar + "]");
+ // jalview.bin.Console.outPrintln("--------------------->[" +
+ // displayChar + "]");
annotationPojo.setDisplayCharacter(displayChar);
if (annotation.colour != null)
{
}
else
{
- jalview.bin.Console.errPrintln("JalviewFileChooser arguments mismatch: "
- + extensions + ", " + descs);
+ jalview.bin.Console
+ .errPrintln("JalviewFileChooser arguments mismatch: "
+ + extensions + ", " + descs);
}
}
}
else
{
- jalview.bin.Console.errPrintln("MSFFile Parser: Can't find sequence for "
- + headers.get(i));
+ jalview.bin.Console
+ .errPrintln("MSFFile Parser: Can't find sequence for "
+ + headers.get(i));
}
}
}
}
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Exception during MSF Checksum calculation");
+ jalview.bin.Console
+ .errPrintln("Exception during MSF Checksum calculation");
e.printStackTrace();
}
}
}
else
{
- jalview.bin.Console.errPrintln("PFAM File reader: Can't find sequence for "
- + headers.get(i));
+ jalview.bin.Console
+ .errPrintln("PFAM File reader: Can't find sequence for "
+ + headers.get(i));
}
}
}
}
}
sqs[i] = new Sequence(id, seq, begin, end);
- if (seq.length()!=(end-begin+1))
+ if (seq.length() != (end - begin + 1))
{
sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
}
{
return 1;
}
-
+
String s1 = ref1.getSource();
String s2 = ref2.getSource();
boolean s1Primary = DBRefSource.isPrimarySource(s1);
String id = null;
for (int i = 0; i < result.size(); i++)
{
- // DEBUG jalview.bin.Console.errPrintln("Processing i'th sequence in Stockholm file")
+ // DEBUG jalview.bin.Console.errPrintln("Processing i'th sequence in
+ // Stockholm file")
RNA current = result.get(i);
String seq = current.getSeq();
String annType = r.stringMatched(1);
String annContent = r.stringMatched(2);
- // jalview.bin.Console.errPrintln("type:" + annType + " content: " + annContent);
+ // jalview.bin.Console.errPrintln("type:" + annType + " content: " +
+ // annContent);
if (annType.equals("GF"))
{
else
{
// throw new IOException("Error parsing " + line);
- jalview.bin.Console.errPrintln(">> missing annotation: " + line);
+ jalview.bin.Console
+ .errPrintln(">> missing annotation: " + line);
}
}
else if (annType.equals("GC"))
processPdbFileWithAnnotate3d(rnaSequences);
} catch (Exception x)
{
- jalview.bin.Console.errPrintln("Exceptions when dealing with RNA in pdb file");
+ jalview.bin.Console
+ .errPrintln("Exceptions when dealing with RNA in pdb file");
x.printStackTrace();
}
}
else
{
- jalview.bin.Console.outPrintln("alignment in document left unchanged.");
+ jalview.bin.Console
+ .outPrintln("alignment in document left unchanged.");
}
}
else
// METHODS)
{
// verify existing alignment sequence annotation is up to date
- jalview.bin.Console.outPrintln("update dataset sequence annotation.");
+ jalview.bin.Console
+ .outPrintln("update dataset sequence annotation.");
}
else
{
// METHODS)
{
// verify existing alignment sequence annotation is up to date
- jalview.bin.Console.outPrintln("update alignment sequence annotation.");
+ jalview.bin.Console
+ .outPrintln("update alignment sequence annotation.");
}
else
{
{
jobComplete = true;
jobsRunning--;
- jalview.bin.Console.errPrintln("WSWUBlastClient error:\n" + exp.toString());
+ jalview.bin.Console
+ .errPrintln("WSWUBlastClient error:\n" + exp.toString());
exp.printStackTrace();
}
}
package jalview.io.exceptions;
/**
- * wrapper for passing error messages and exceptions back to UI when image io goes wrong
+ * wrapper for passing error messages and exceptions back to UI when image io
+ * goes wrong
+ *
* @author jprocter
*
*/
}
else if (!"+".equals(strand))
{
- jalview.bin.Console.errPrintln("Strand must be specified for alignment");
+ jalview.bin.Console
+ .errPrintln("Strand must be specified for alignment");
return;
}
String[] tokens = region.split(" ");
if (tokens.length != 3)
{
- jalview.bin.Console.errPrintln("Malformed Align descriptor: " + region);
+ jalview.bin.Console
+ .errPrintln("Malformed Align descriptor: " + region);
return null;
}
return true;
}
}
- jalview.bin.Console.errPrintln("Sorry, I don't handle exonerate model " + model);
+ jalview.bin.Console
+ .errPrintln("Sorry, I don't handle exonerate model " + model);
return false;
}
}
} catch (NumberFormatException nfe)
{
- jalview.bin.Console.errPrintln("Invalid start or end in Target " + target);
+ jalview.bin.Console
+ .errPrintln("Invalid start or end in Target " + target);
}
}
*/
if (!trimMapping(from, to, fromRatio, toRatio))
{
- jalview.bin.Console.errPrintln("Ignoring mapping from " + Arrays.toString(from)
- + " to " + Arrays.toString(to) + " as counts don't match!");
+ jalview.bin.Console.errPrintln(
+ "Ignoring mapping from " + Arrays.toString(from) + " to "
+ + Arrays.toString(to) + " as counts don't match!");
return null;
}
return sf;
} catch (NumberFormatException nfe)
{
- jalview.bin.Console.errPrintln("Invalid number in gff: " + nfe.getMessage());
+ jalview.bin.Console
+ .errPrintln("Invalid number in gff: " + nfe.getMessage());
return null;
}
}
fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Couldn't handle datasource of type " + jtype
- + " using URI " + file);
+ jalview.bin.Console
+ .errPrintln("Couldn't handle datasource of type " + jtype
+ + " using URI " + file);
e.printStackTrace();
return;
}
{
for (Object o : newdm)
{
- jalview.bin.Console.outPrintln("Will need to create an " + o.getClass());
+ jalview.bin.Console
+ .outPrintln("Will need to create an " + o.getClass());
}
// now test uniquify/deuniquify stuff
}
else
{
- jalview.bin.Console.errPrintln("WARNING: Unassociated treeNode "
- + tnode.element().toString() + " "
- + ((tnode.getName() != null)
- ? " label " + tnode.getName()
- : ""));
+ jalview.bin.Console
+ .errPrintln("WARNING: Unassociated treeNode "
+ + tnode.element().toString() + " "
+ + ((tnode.getName() != null)
+ ? " label " + tnode.getName()
+ : ""));
}
}
}
initialise(vcfFile);
} catch (IOException e)
{
- jalview.bin.Console.errPrintln("Error opening VCF file: " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error opening VCF file: " + e.getMessage());
}
// map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
}
} catch (Throwable e)
{
- jalview.bin.Console.errPrintln("Error processing VCF: " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error processing VCF: " + e.getMessage());
e.printStackTrace();
if (gui != null)
{
jsex[0] = jex;
if (jvlite.debug)
{
- jalview.bin.Console.errPrintln("Falling back to javascript: url call");
+ jalview.bin.Console
+ .errPrintln("Falling back to javascript: url call");
}
StringBuffer sb = new StringBuffer(
"javascript:" + _listener + "(");
;
}
- jalview.bin.Console.errPrintln("Relaying selection to jsfunction:" + _listener);
+ jalview.bin.Console
+ .errPrintln("Relaying selection to jsfunction:" + _listener);
executeJavascriptFunction(_listener,
new Object[]
{ src, setid, jvlite.arrayToSeparatorList(seqs),
"" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Couldn't execute callback with " + _listenerfn
- + " for atomSpec: " + atom);
+ jalview.bin.Console.errPrintln("Couldn't execute callback with "
+ + _listenerfn + " for atomSpec: " + atom);
ex.printStackTrace();
}
}
executeJavascriptFunction(true, _listenerfn, st);
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Couldn't execute callback with " + _listenerfn
- + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
- + "," + st[3] + "}"); // + ","+st[4]+"\n");
+ jalview.bin.Console.errPrintln("Couldn't execute callback with "
+ + _listenerfn + " using args { " + st[0] + ", " + st[1]
+ + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
ex.printStackTrace();
}
inputURLMenuItem_actionPerformed(null);
} catch (FileFormatException e1)
{
- jalview.bin.Console.errPrintln("Error loading from URL: " + e1.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error loading from URL: " + e1.getMessage());
}
}
});
Float floatValue = Float.valueOf(degrees);
if (cachedRotations.get(axis).containsKey(floatValue))
{
- // jalview.bin.Console.outPrintln("getRotation from cache: " + (int) degrees);
+ // jalview.bin.Console.outPrintln("getRotation from cache: " + (int)
+ // degrees);
return cachedRotations.get(axis).get(floatValue);
}
* entry names
*/
private Map<RnaModel, String> rnaSessions = new HashMap<>();
-
+
/**
* map from contact matrices to their XML ids
*/
- private Map<ContactMatrixI,String> contactMatrices = new HashMap<>();
+ private Map<ContactMatrixI, String> contactMatrices = new HashMap<>();
+
private Map<String, ContactMatrixI> contactMatrixRefs = new HashMap<>();
- private List<jalview.xml.binding.jalview.MatrixType> xmlMatrices= new ArrayList<>();
+
+ private List<jalview.xml.binding.jalview.MatrixType> xmlMatrices = new ArrayList<>();
/**
* A helper method for safely using the value of an optional attribute that
}
/**
- * base class for resolving forward references to an as-yet unmarshalled object referenced by already unmarshalled objects
+ * base class for resolving forward references to an as-yet unmarshalled
+ * object referenced by already unmarshalled objects
*
* @author jprocter
*
*/
- abstract class forwardRef {
+ abstract class forwardRef
+ {
String sref;
String type;
}
public abstract boolean isResolvable();
+
/**
* @return true if the forward reference was fully resolved
*/
return type + " reference to " + sref;
}
}
+
/**
* resolve forward references to sequences by their ID
+ *
* @author jprocter
*/
abstract class SeqFref extends forwardRef
{
super(_sref, type);
}
+
public SequenceI getSrefSeq()
{
return seqRefIds.get(sref);
};
return fref;
}
-
+
public forwardRef newMatrixFref(final String matRef,
final jalview.util.MapList mapping, final AlignmentAnnotation jaa)
{
view.setShowFullId(av.getShowJVSuffix());
view.setRightAlignIds(av.isRightAlignIds());
view.setIdWidth(av.getIdWidth());
- view.setIdWidthManuallyAdjusted(ap.getIdPanel().getIdCanvas().isManuallyAdjusted());
-
+ view.setIdWidthManuallyAdjusted(
+ ap.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
view.setShowSequenceFeatures(av.isShowSequenceFeatures());
view.setShowText(av.getShowText());
view.setShowUnconserved(av.getShowUnconserved());
// jms.addViewport(view);
object.getViewport().add(view);
}
-
-
+
if (storeDS)
{
// store matrices referenced by any views or annotation in this dataset
- if (xmlMatrices!=null && xmlMatrices.size()>0)
+ if (xmlMatrices != null && xmlMatrices.size() > 0)
{
- Console.debug("Adding "+xmlMatrices.size()+" matrices to dataset.");
+ Console.debug(
+ "Adding " + xmlMatrices.size() + " matrices to dataset.");
vamsasSet.getMatrix().addAll(xmlMatrices);
xmlMatrices.clear();
}
}
-
// object.setJalviewModelSequence(jms);
// object.getVamsasModel().addSequenceSet(vamsasSet);
object.getVamsasModel().getSequenceSet().add(vamsasSet);
.getContactMatrixFor(annotation);
if (cm != null)
{
- storeMatrixFor(vamsasSet, an,annotation, cm);
+ storeMatrixFor(vamsasSet, an, annotation, cm);
}
}
}
}
- private void storeMatrixFor(SequenceSet root, Annotation an, AlignmentAnnotation annotation, ContactMatrixI cm)
+ private void storeMatrixFor(SequenceSet root, Annotation an,
+ AlignmentAnnotation annotation, ContactMatrixI cm)
{
String cmId = contactMatrices.get(cm);
- MatrixType xmlmat=null;
-
+ MatrixType xmlmat = null;
+
// first create an xml ref for the matrix data, if none exist
if (cmId == null)
{
{
xmlmat.setCutHeight(cm.getCutHeight());
}
- xmlmat.setId(cmId = "m"+contactMatrices.size()+System.currentTimeMillis());
- Console.trace("Matrix data stored :"+cmId);
+ xmlmat.setId(cmId = "m" + contactMatrices.size()
+ + System.currentTimeMillis());
+ Console.trace("Matrix data stored :" + cmId);
contactMatrices.put(cm, cmId);
contactMatrixRefs.put(cmId, cm);
xmlMatrices.add(xmlmat);
- } else {
- Console.trace("Existing Matrix stored :"+cmId);
+ }
+ else
+ {
+ Console.trace("Existing Matrix stored :" + cmId);
}
// now store mapping
MapOnAMatrixType xmlmatmapping = new MapOnAMatrixType();
xmlmatmapping.setMatrix(cmId);
-
+
// Pretty much all matrices currently managed in this way are
// mappableContactMatrixI implementations - but check anyway
if (cm instanceof MappableContactMatrixI)
initSeqRefs();
}
AlignFrame af = null, _af = null;
- List<AlignFrame> toRepaint=new ArrayList<AlignFrame>();
+ List<AlignFrame> toRepaint = new ArrayList<AlignFrame>();
IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
final String file = jprovider.getFilename();
} while (jarentry != null);
jin.close();
resolveFrefedSequences();
- for (AlignFrame alignFrame:toRepaint)
+ for (AlignFrame alignFrame : toRepaint)
{
alignFrame.repaint();
}
// ////////////////////////////////
// LOAD MATRICES (IF ANY)
-
- if (vamsasSet.getMatrix()!=null && vamsasSet.getMatrix().size()>0)
+
+ if (vamsasSet.getMatrix() != null && vamsasSet.getMatrix().size() > 0)
{
importMatrixData(vamsasSet.getMatrix());
}
-
+
// ////////////////////////////////
// LOAD SEQUENCES
for (MapOnAMatrixType xmlmat : annotation.getContactmatrix())
{
restoreMatrixFor(jaa.sequenceRef, jaa, xmlmat);
- }
+ }
}
}
private void importMatrixData(List<MatrixType> xmlmatrices)
{
- for (MatrixType xmlmat:xmlmatrices)
+ for (MatrixType xmlmat : xmlmatrices)
{
if (!PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType()))
{
- Console.error("Ignoring matrix '"+xmlmat.getId()+"' of type '"+xmlmat.getType());
+ Console.error("Ignoring matrix '" + xmlmat.getId() + "' of type '"
+ + xmlmat.getType());
continue;
}
continue;
}
- float[][] elements = ContactMatrix
- .fromFloatStringToContacts(xmlmat.getElements(),
- xmlmat.getCols().intValue(),
- xmlmat.getRows().intValue());
-
+ float[][] elements = ContactMatrix.fromFloatStringToContacts(
+ xmlmat.getElements(), xmlmat.getCols().intValue(),
+ xmlmat.getRows().intValue());
+
List<BitSet> newgroups = new ArrayList<BitSet>();
if (xmlmat.getGroups().size() > 0)
{
newgroups.add(deStringifyBitset(sgroup));
}
}
- String nwk = xmlmat.getNewick().size() > 0
- ? xmlmat.getNewick().get(0)
+ 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");
+ Console.log
+ .info("Ignoring additional clusterings for contact matrix");
}
String treeMethod = xmlmat.getTreeMethod();
- double thresh = xmlmat.getCutHeight() != null
- ? xmlmat.getCutHeight()
+ double thresh = xmlmat.getCutHeight() != null ? xmlmat.getCutHeight()
: 0;
GroupSet grpset = new GroupSet();
grpset.restoreGroups(newgroups, treeMethod, nwk, thresh);
-
+
FloatContactMatrix newcm = new FloatContactMatrix(elements, grpset);
contactMatrixRefs.put(xmlmat.getId(), newcm);
- Console.trace("Restored base contact matrix "+xmlmat.getId());
+ Console.trace("Restored base contact matrix " + xmlmat.getId());
}
}
private void restoreMatrixFor(SequenceI sequenceRef,
AlignmentAnnotation jaa, MapOnAMatrixType xmlmatmapping)
- {
+ {
// restore mapping data to matrix data
jalview.util.MapList mapping = null;
if (xmlmatmapping.getMapping() != null)
mapping = new jalview.util.MapList(fr, fto,
m.getMapFromUnit().intValue(), m.getMapToUnit().intValue());
}
-
+
// locate matrix data in project XML and import
ContactMatrixI cm = contactMatrixRefs.get(xmlmatmapping.getMatrix());
if (cm == null)
}
af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
safeInt(view.getWidth()), safeInt(view.getHeight()));
-
- af.alignPanel.fontChanged(); // make sure font is updated *before* we set ID width
- if (view.getIdWidth()==null)
+
+ af.alignPanel.fontChanged(); // make sure font is updated *before* we set ID
+ // width
+ if (view.getIdWidth() == null)
{
- if (!isVersionStringLaterThan("2.11.3", jm.getVersion())) {
+ if (!isVersionStringLaterThan("2.11.3", jm.getVersion()))
+ {
// Pre 2.11.3 jalview projects do not store the id width
// idWidth was also calculated in a different way.
viewport.setIdWidth(af.alignPanel.getLegacyIdWidth());
af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(true);
}
- } else {
+ }
+ else
+ {
viewport.setIdWidth(view.getIdWidth());
- af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(view.isIdWidthManuallyAdjusted());
+ af.alignPanel.getIdPanel().getIdCanvas()
+ .setManuallyAdjusted(view.isIdWidthManuallyAdjusted());
}
-
+
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
: row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || dc != row_annotations[sCol - 1].secondaryStructure || !validEnd;
+ || dc != row_annotations[sCol - 1].secondaryStructure
+ || !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| dc != row_annotations[column].secondaryStructure;
: row_annotations[column - 1].displayCharacter;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter) || !validEnd;
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter)
+ || !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
* number of contacts for each pixel_step - to last whole contact
*/
final double contacts_step;
-
+
final int lastStep;
/**
* Bean used to map from a range of contacts to a range of pixels
+ *
* @param contacts
- * @param graphHeight Number of pixels to map given range of contacts
+ * @param graphHeight
+ * Number of pixels to map given range of contacts
*/
public ContactGeometry(final ContactListI contacts, int graphHeight)
{
pixels_step = (int) Math
.ceil(((double) graphHeight) / (double) contact_height);
}
- contacts_step = pixels_step*contacts_per_pixel;
- lastStep = (int) Math.min((double)graphHeight, ((double)graphHeight)/((double)pixels_step));
+ contacts_step = pixels_step * contacts_per_pixel;
+ lastStep = (int) Math.min((double) graphHeight,
+ ((double) graphHeight) / ((double) pixels_step));
}
public class contactInterval
return cStart == them.cStart && cEnd == them.cEnd && pEnd == them.pEnd
&& pStart == them.pStart;
}
+
@Override
public String toString()
{
- return "Contacts ["+cStart+","+cEnd+"] : Pixels ["+pStart+","+pEnd+"]";
+ return "Contacts [" + cStart + "," + cEnd + "] : Pixels [" + pStart
+ + "," + pEnd + "]";
}
}
{
// TODO: turn into function on hiddenColumns and create test !!
Iterator<int[]> viscont = hiddenColumns.getVisContigsIterator(
- -1+mappedRange[p], -1+mappedRange[p + 1], false);
+ -1 + mappedRange[p], -1 + mappedRange[p + 1], false);
containsHidden = !viscont.hasNext();
if (!containsHidden)
{
}
else
{
- rowsel = columnSelection.intersects(-1+mappedRange[p],
- -1+mappedRange[p + 1]);
+ rowsel = columnSelection.intersects(-1 + mappedRange[p],
+ -1 + mappedRange[p + 1]);
}
}
return rowsel;
* 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
*/
/**
*
- * @param no_data - colour when no data available
- * @param hidden - colour if this row is hidden
- * @param maxColor - colour for maximum value of contact
- * @param minColor - colour for minimum value of contact
- * @param selMinColor - min colour if the contact has been selected
- * @param selMaxColor - max colour if contact is selected
+ * @param no_data
+ * - colour when no data available
+ * @param hidden
+ * - colour if this row is hidden
+ * @param maxColor
+ * - colour for maximum value of contact
+ * @param minColor
+ * - colour for minimum value of contact
+ * @param selMinColor
+ * - min colour if the contact has been selected
+ * @param selMaxColor
+ * - max colour if contact is selected
*/
public Shading(Color no_data, Color hidden, Color maxColor,
Color minColor, Color selMinColor, Color selMaxColor)
return new Shading(Color.pink, Color.red,
new Color(247, 252, 245), new Color(0, 68, 28),
- new Color(28, 0, 68), new Color(245,247,252));
+ new Color(28, 0, 68), new Color(245, 247, 252));
}
};
}
HiddenColumns hiddenColumns, ColumnSelection columnSelection,
AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
int eRes, float min, float max, int y)
- {
+ {
if (sRes > aa_annotations.length)
{
return;
// uncomment below to render whole area of matrix as pink
// g.setColor(shade.no_data);
- // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth, _aa.graphHeight);
-
+ // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth,
+ // _aa.graphHeight);
+
boolean showGroups = _aa.isShowGroupsForContactMatrix();
int column;
int aaMax = aa_annotations.length - 1;
ContactMatrixI cm = viewport.getContactMatrix(_aa);
- if (cm==null)
+ if (cm == null)
{
return;
}
g.setColor(col);
if (cgeom.pixels_step > 1)
{
- g.fillRect(x * charWidth, botY+ht, charWidth, cgeom.pixels_step);
+ g.fillRect(x * charWidth, botY + ht, charWidth,
+ cgeom.pixels_step);
}
else
{
- g.drawLine(x * charWidth, botY+ht, (x + 1) * charWidth, botY+ht);
+ g.drawLine(x * charWidth, botY + ht, (x + 1) * charWidth,
+ botY + ht);
}
}
x++;
} catch (Exception ex)
{
// used to try to parse a V1 Castor generated colours file
- jalview.bin.Console.errPrintln("Failed to read colour scheme from " + filePath
- + " : " + ex.toString());
+ jalview.bin.Console.errPrintln("Failed to read colour scheme from "
+ + filePath + " : " + ex.toString());
}
return ucs;
cs.getSchemeClass().getDeclaredConstructor().newInstance());
} catch (InstantiationException | IllegalAccessException e)
{
- jalview.bin.Console.errPrintln("Error instantiating colour scheme for "
- + cs.toString() + " " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error instantiating colour scheme for "
+ + cs.toString() + " " + e.getMessage());
e.printStackTrace();
} catch (ReflectiveOperationException roe)
{
this.mask = setNums(s);
// for (int i=0; i < mask.length; i++) {
- // jalview.bin.Console.outPrintln(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+ // jalview.bin.Console.outPrintln(mask[i] + " " +
+ // ResidueProperties.aa[mask[i]]);
// }
}
if (tot > ((threshold * size) / 100))
{
- // jalview.bin.Console.outPrintln("True conserved "+tot+" from "+threshold+" out of
+ // jalview.bin.Console.outPrintln("True conserved "+tot+" from
+ // "+threshold+" out of
// "+size+" : "+maskstr);
return true;
}
for (int x = 0; x < this.annotation._rnasecstr.length; x++)
{
- // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
+ // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin"
+ // +
// this.annotation._rnasecstr[x].getBegin());
// jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
// pairs.put(this.annotation._rnasecstr[x].getBegin(),
currentColour = helixcolorhash.get(currentHelix);
}
- // jalview.bin.Console.outPrintln(c + " " + j + " helix " + currentHelix + " " +
+ // jalview.bin.Console.outPrintln(c + " " + j + " helix " + currentHelix + "
+ // " +
// currentColour);
return currentColour;
}
featureColour.setThreshold(Float.valueOf(tval).floatValue());
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Couldn't parse threshold value as a float: ("
- + tval + ")");
+ jalview.bin.Console
+ .errPrintln("Couldn't parse threshold value as a float: ("
+ + tval + ")");
}
}
if (gcol.hasMoreTokens())
jalview.bin.Console.outPrintln(", ");
}
}
- jalview.bin.Console.outPrintln("]" + (res.hasMoreElements() ? "," : ""));
+ jalview.bin.Console
+ .outPrintln("]" + (res.hasMoreElements() ? "," : ""));
}
jalview.bin.Console.outPrintln("};");
}
private List<String> parameters;
- private boolean waitNeeded=false;
+ private boolean waitNeeded = false;
+
public StructureCommand(String cmd, String... params)
{
command = cmd;
}
}
}
-
+
public void setWaitNeeded(boolean wait)
{
- waitNeeded=wait;
+ waitNeeded = wait;
}
-
+
@Override
public boolean isWaitNeeded()
{
return waitNeeded;
}
-
+
@Override
public void addParameter(String param)
{
boolean hasParameters();
- default boolean isWaitNeeded() { return false; };
+ default boolean isWaitNeeded()
+ {
+ return false;
+ };
}
{
return null;
}
-
+
@Override
public StructureCommandI restoreSession(String filePath)
{
* @return
*/
StructureCommandI openSession(String filepath);
-
+
/**
- * Returns command to restore a previously saved version of an existing structure viewer session file.
- * Default implementation calls 'openSession'
+ * Returns command to restore a previously saved version of an existing
+ * structure viewer session file. Default implementation calls 'openSession'
+ *
* @param filePath
* @return
*/
StructureCommandI restoreSession(String filePath);
-
/**
* Returns a command to ask the viewer to close down
*
List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues);
- default List<StructureCommandI> showHetatms(List<String> toShow) {
+ default List<StructureCommandI> showHetatms(List<String> toShow)
+ {
return Collections.EMPTY_LIST;
}
}
{
if (mappings.isEmpty())
{
- jalview.bin.Console.errPrintln("reportMapping: No PDB/Sequence mappings.");
+ jalview.bin.Console
+ .errPrintln("reportMapping: No PDB/Sequence mappings.");
}
else
{
int i = 0;
for (StructureMapping sm : mappings)
{
- jalview.bin.Console.errPrintln("mapping " + i++ + " : " + sm.pdbfile);
+ jalview.bin.Console
+ .errPrintln("mapping " + i++ + " : " + sm.pdbfile);
}
}
}
pdbFile, sourceType, tft, paeFilename, true);
}
-
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol). Either constructs a mapping
* - structure data resource
* @param sourceType
* - how to resolve data from resource
- * @param tft - specify how to interpret the temperature factor column in the atom data
- * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
- * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray
+ * @param tft
+ * - specify how to interpret the temperature factor column in the
+ * atom data
+ * @param paeFilename
+ * - when not null, specifies a filename containing a matrix
+ * formatted in JSON using one of the known PAE formats
+ * @param doXferSettings
+ * - when true, transfer annotation to mapped sequences in
+ * sequenceArray
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(boolean forStructureView,
* @param IProgressIndicator
* reference to UI component that maintains a progress bar for the
* mapping operation
- * @param tft - specify how to interpret the temperature factor column in the atom data
- * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
- * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray
+ * @param tft
+ * - specify how to interpret the temperature factor column in the
+ * atom data
+ * @param paeFilename
+ * - when not null, specifies a filename containing a matrix
+ * formatted in JSON using one of the known PAE formats
+ * @param doXferSettings
+ * - when true, transfer annotation to mapped sequences in
+ * sequenceArray
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile computeMapping(boolean forStructureView,
{
for (int s : cs.getSelected())
{
- matched.set(s);
+ matched.set(s);
}
}
else
return f;
}
-
/**
* Use restoreSession when you want to restore a previously saved sesssion to
* the running viewer instance.
public void restoreSession(String absolutePath)
{
String prefix = getViewerType().toString();
- try {
+ try
+ {
StructureCommandI cmd = commandGenerator.restoreSession(absolutePath);
if (cmd != null)
/**
* list the ligands available for display/hiding in the current view
+ *
* @return HETATM CODE:Molecule name
*/
- public Map<String, String> getHetatmNames() {
+ public Map<String, String> getHetatmNames()
+ {
return Collections.EMPTY_MAP;
}
+
/**
* Generates and executes a command to show the given hetatm types as CPK
*
- * @param toShow - one or more of strings from getHetatmNames
+ * @param toShow
+ * - one or more of strings from getHetatmNames
*/
public void showHetatms(List<String> toShow)
{
- executeCommands(commandGenerator.showHetatms(toShow), false, "Adjusting hetatm visibility");
+ executeCommands(commandGenerator.showHetatms(toShow), false,
+ "Adjusting hetatm visibility");
}
}
// BH 2018 -- added more valuable report
if (errorMessage != null)
{
- jalview.bin.Console.errPrintln("IdentifiersUrlProvider: cannot read " + idFileName
- + ": " + errorMessage);
+ jalview.bin.Console.errPrintln("IdentifiersUrlProvider: cannot read "
+ + idFileName + ": " + errorMessage);
}
return idData;
}
if (channelPropsURL == null)
{
// complete failure of channel_properties, set all properties to defaults
- jalview.bin.Console.errPrintln("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
- + "' file at '"
+ jalview.bin.Console.errPrintln("Failed to find '/"
+ + CHANNEL_PROPERTIES_FILENAME + "' file at '"
+ (channelPropsURL == null ? "null"
: channelPropsURL.toString())
+ "'. Using class defaultProps.");
}
else
{
- jalview.bin.Console.errPrintln("Failed to get channel property '" + key + "'");
+ jalview.bin.Console
+ .errPrintln("Failed to get channel property '" + key + "'");
}
}
return null;
return color;
}
-
+
/**
*
* @return random color
(int) (Math.random() * 255), (int) (Math.random() * 255));
return col;
}
+
/**
* Convert to Tk colour code format
*
}
/**
- * Bespoke method to format a percentage (or any other) float value to the specified number of
- * decimal places. Avoids use of general-purpose format parsers as a
- * processing hotspot.
+ * Bespoke method to format a percentage (or any other) float value to the
+ * specified number of decimal places. Avoids use of general-purpose format
+ * parsers as a processing hotspot.
*
* @param sb
* @param value
}
else
{
- jalview.bin.Console.outPrintln("Created a url from " + ((int[]) url[0])[0]
- + "out of " + idstring[0].length + " sequences.");
+ jalview.bin.Console
+ .outPrintln("Created a url from " + ((int[]) url[0])[0]
+ + "out of " + idstring[0].length + " sequences.");
jalview.bin.Console.outPrintln("Sequences that did not match:");
for (int sq = 0; sq < idstring[0].length; sq++)
{
if (!((boolean[]) url[1])[sq])
{
- jalview.bin.Console.outPrintln("Seq " + sq + ": " + idstring[0][sq] + "\t: "
- + idstring[1][sq]);
+ jalview.bin.Console.outPrintln("Seq " + sq + ": "
+ + idstring[0][sq] + "\t: " + idstring[1][sq]);
}
}
jalview.bin.Console.outPrintln("Sequences that DID match:");
{
if (((boolean[]) url[1])[sq])
{
- jalview.bin.Console.outPrintln("Seq " + sq + ": " + idstring[0][sq] + "\t: "
- + idstring[1][sq]);
+ jalview.bin.Console.outPrintln("Seq " + sq + ": "
+ + idstring[0][sq] + "\t: " + idstring[1][sq]);
}
}
jalview.bin.Console.outPrintln("The generated URL:");
jalview.bin.Console.outPrintln(
"Link " + i + " " + links[i] + " : " + ul.toString());
jalview.bin.Console.outPrintln(" pref : " + ul.getUrl_prefix());
- jalview.bin.Console.outPrintln(" IdReplace : " + ul.getIDRegexReplace());
- jalview.bin.Console.outPrintln(" SeqReplace : " + ul.getSeqRegexReplace());
+ jalview.bin.Console
+ .outPrintln(" IdReplace : " + ul.getIDRegexReplace());
+ jalview.bin.Console
+ .outPrintln(" SeqReplace : " + ul.getSeqRegexReplace());
jalview.bin.Console.outPrintln(" Suffixes : " + ul.getUrl_suffix());
jalview.bin.Console.outPrintln(
}
else
{
- jalview.bin.Console.errPrintln("Invalid URLLink : " + links[i] + " : "
- + ul.getInvalidMessage());
+ jalview.bin.Console.errPrintln("Invalid URLLink : " + links[i]
+ + " : " + ul.getInvalidMessage());
}
}
}
return -4;
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln("Could not parse JAVA_COMPILE_VERSION");
+ jalview.bin.Console
+ .errPrintln("Could not parse JAVA_COMPILE_VERSION");
return -5;
}
init = true;
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Problems initializing the log4j system\n");
+ jalview.bin.Console
+ .errPrintln("Problems initializing the log4j system\n");
e.printStackTrace(System.err);
}
}
}
if (msg != null)
{
- jalview.bin.Console.errPrintln("Platform: timer mark\t" + ((t - time) / 1000f)
- + "\t" + ((t - mark) / 1000f) + "\t" + msg);
+ jalview.bin.Console.errPrintln(
+ "Platform: timer mark\t" + ((t - time) / 1000f) + "\t"
+ + ((t - mark) / 1000f) + "\t" + msg);
}
mark = t;
}
case TIME_GET:
if (msg != null)
{
- jalview.bin.Console.errPrintln("Platform: timer dur\t" + ((t - time) / 1000f)
- + "\t" + ((duration) / 1000f) + "\t" + msg);
+ jalview.bin.Console
+ .errPrintln("Platform: timer dur\t" + ((t - time) / 1000f)
+ + "\t" + ((duration) / 1000f) + "\t" + msg);
}
set = 0;
break;
* @j2sNative var a =
* decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
* + "?").split("?")[1].split("#")[0]); a &&
- * (jalview.bin.Console.outPrintln("URL arguments detected were "+a)) &&
- * (J2S.thisApplet.__Info.urlargs = a.split(" "));
+ * (jalview.bin.Console.outPrintln("URL arguments detected were
+ * "+a)) && (J2S.thisApplet.__Info.urlargs = a.split(" "));
* (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args
* == "" || J2S.thisApplet.__Info.args == "??") &&
- * (J2S.thisApplet.__Info.args = a) && (jalview.bin.Console.outPrintln("URL
- * arguments were passed to J2S main."));
+ * (J2S.thisApplet.__Info.args = a) &&
+ * (jalview.bin.Console.outPrintln("URL arguments were passed
+ * to J2S main."));
*/
} catch (Throwable t)
{
// debug
for (int s = 0; s <= rg.numSubs(); s++)
{
- jalview.bin.Console.errPrintln("Sub " + s + " : " + rg.matchedFrom(s)
- + " : " + rg.matchedTo(s) + " : '"
+ jalview.bin.Console.errPrintln("Sub " + s + " : "
+ + rg.matchedFrom(s) + " : " + rg.matchedTo(s) + " : '"
+ rg.stringMatched(s) + "'");
}
// try to collate subgroup matches
}
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
- // jalview.bin.Console.errPrintln("grey out ("+alignmentAnnotation.label+")");
+ // jalview.bin.Console.errPrintln("grey out
+ // ("+alignmentAnnotation.label+")");
return true;
}
return false;
if (aa.graph > 0)
{
- aa.height += aa.graphHeight+20;
+ aa.height += aa.graphHeight + 20;
}
if (aa.height == 0)
{
if (this == av)
{
- jalview.bin.Console.errPrintln("Ignoring recursive setCodingComplement request");
+ jalview.bin.Console
+ .errPrintln("Ignoring recursive setCodingComplement request");
}
else
{
*/
public void setStartEndSeq(int start, int end)
{
- // jalview.bin.Console.outPrintln("ViewportRange setStartEndSeq " + start + " " + end);
+ // jalview.bin.Console.outPrintln("ViewportRange setStartEndSeq " + start +
+ // " " + end);
int[] oldvalues = updateStartEndSeq(start, end);
int oldstartseq = oldvalues[0];
int oldendseq = oldvalues[1];
{
vpstart = visHeight - h;
}
- // jalview.bin.Console.outPrintln("ViewportRanges setviewportStartAndHeight " + vpstart
+ // jalview.bin.Console.outPrintln("ViewportRanges setviewportStartAndHeight
+ // " + vpstart
// + " " + start + " " + h + " " + getVisibleAlignmentHeight());
setStartEndSeq(vpstart, vpstart + h - 1);
{
synchronized (inProgress)
{
- // jalview.bin.Console.errPrintln("Worker " + worker + " marked as complete.");
+ // jalview.bin.Console.errPrintln("Worker " + worker + " marked as
+ // complete.");
inProgress.remove(worker);
List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
if (upd != null)
@Override
public boolean isWorking()
{
- boolean working=false;
+ boolean working = false;
synchronized (inProgress)
{
// jalview.bin.Console.errPrintln("isWorking "+hashCode());
{
for (List<AlignCalcWorkerI> workers : workersLists)
{
- if (workers!=null)
+ if (workers != null)
{
- synchronized (workers) {
+ synchronized (workers)
+ {
working |= workers.size() > 0;
}
}
}
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Couldn't locate PICR service instance.\n");
+ jalview.bin.Console
+ .errPrintln("Couldn't locate PICR service instance.\n");
e.printStackTrace();
}
while (sdataset.size() > 0 && db < dbSources.length)
{
int maxqlen = 1; // default number of queries made at one time
- jalview.bin.Console.outPrintln("Verifying against " + dbSources[db].getDbName());
+ jalview.bin.Console
+ .outPrintln("Verifying against " + dbSources[db].getDbName());
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
}
}
- jalview.bin.Console.outPrintln("Adding dbrefs to " + sequence.getName()
- + " from " + dbSource + " sequence : "
+ jalview.bin.Console.outPrintln("Adding dbrefs to "
+ + sequence.getName() + " from " + dbSource + " sequence : "
+ retrievedSeq.getName());
sequence.transferAnnotation(retrievedSeq, mp);
}
// } catch (OutOfMemoryError e)
// {
- // jalview.bin.Console.errPrintln("Out of memory when displaying status. Squashing
+ // jalview.bin.Console.errPrintln("Out of memory when displaying status.
+ // Squashing
// error.");
// wsInfo.appendProgressText(j.jobnum,
// "..\n(Out of memory when displaying status)\n");
MapList getMapFor(SequenceI sequenceRef);
/**
- * Locate a position in the mapped sequence for a single column in the matrix.
+ * Locate a position in the mapped sequence for a single column in the matrix.
* this to resolve positions corresponding to column clusters
*
* @param localFrame
int[] getMappedPositionsFor(SequenceI localFrame, int column);
/**
- * Locate a position in the mapped sequence for a contiguous range of columns in the matrix
- * use this to resolve positions corresponding to column clusters
+ * Locate a position in the mapped sequence for a contiguous range of columns
+ * in the matrix use this to resolve positions corresponding to column
+ * clusters
*
* @param localFrame
* - sequence derivced from reference sequence
/**
* the matrix that is being mapped to
*/
- protected ContactMatrixI mappedMatrix=null;
-
+ protected ContactMatrixI mappedMatrix = null;
+
public ContactListI getContactList(int column)
{
return mappedMatrix.getContactList(column);
{
return mappedMatrix;
}
-
+
@Override
public GroupSetI getGroupSet()
{
{
mappedMatrix.setGroupSet(makeGroups);
}
-
+
/**
* the sequence and how it is mapped to the matrix
*/
+ "' is not mappable for the given localFrame sequence. ("
+ localFrame.getName() + ")");
}
-
+
// now look up from-to matrix columns in toSeq frame
-
+
if (toSeq == null)
{
// no mapping - so we assume 1:1
// first locate on reference sequence
int[] mappedPositions = toSeq.locateInFrom(from, to);
- if (mappedPositions==null)
+ if (mappedPositions == null)
{
return null;
}
-
+
// and now map to localFrame
// from-to columns on the associated sequence should be
// i. restricted to positions in localFrame
- // ii.
-
-// 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]);
-// }
-// }
-// int[] _trimmed = new int[e - s + 1];
-// return _trimmed;
+ // ii.
+
+ // 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]);
+ // }
+ // }
+ // int[] _trimmed = new int[e - s + 1];
+ // return _trimmed;
return mappedPositions;
}
}
/**
- * get a specific element of the underlying contact matrix in its data-local coordinates
- * rather than the mapped frame. Implementations are allowed to throw
- * RunTimeExceptions if _column/i are out of bounds
+ * get a specific element of the underlying contact matrix in its data-local
+ * coordinates rather than the mapped frame. Implementations are allowed to
+ * throw RunTimeExceptions if _column/i are out of bounds
*
* @param _column
* @param i
* @return
*/
- public double getElementAt(int _column, int i) {
+ public double getElementAt(int _column, int i)
+ {
return mappedMatrix.getElementAt(_column, i);
}
MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
{
-
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
throws FileFormatException
*/
public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
{
- mappedMatrix=new FloatContactMatrix(matrix);
+ mappedMatrix = new FloatContactMatrix(matrix);
setRefSeq(_refSeq);
}
public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
float[][] elements2, GroupSet grps2)
{
- this(newRefSeq, new FloatContactMatrix(elements2,grps2));
+ this(newRefSeq, new FloatContactMatrix(elements2, grps2));
toSeq = newFromMapList;
}
mappedMatrix = floatContactMatrix;
setRefSeq(_refSeq);
}
+
public PAEContactMatrix(SequenceI _refSeq, MapList newFromMapList,
ContactMatrixI floatContactMatrix)
{
setRefSeq(_refSeq);
toSeq = newFromMapList;
}
-
+
@Override
protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
MapList newFromMapList)
row++;
col = 0;
}
- mappedMatrix=new FloatContactMatrix(elements);
+ mappedMatrix = new FloatContactMatrix(elements);
}
/**
Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
// two pass - to allocate the elements array
-
- int maxrow=-1,maxcol=-1;
+
+ int maxrow = -1, maxcol = -1;
while (rows.hasNext())
{
int row = rows.next().intValue();
{
maxcol = col;
}
- elements[col - 1][row-1] = escore;
+ elements[col - 1][row - 1] = escore;
}
- mappedMatrix=new FloatContactMatrix(elements);
+ mappedMatrix = new FloatContactMatrix(elements);
}
@Override
return PAEMATRIX;
}
-
public static void validateContactMatrixFile(String fileName)
throws FileFormatException, IOException
{
"No data in PAE matrix read from '" + fileName + "'");
}
}
+
@Override
public boolean equals(Object obj)
{
return super.equals(obj);
}
+
@Override
public int hashCode()
{
}
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Warning: problems reading temp file " + file);
+ jalview.bin.Console
+ .errPrintln("Warning: problems reading temp file " + file);
return null;
}
return bf;
System.err
.println("Please report the following to help@jalview.org :");
jalview.bin.Console.errPrintln("EMBL Record " + accession);
- jalview.bin.Console.errPrintln("Resulted in exception: " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("Resulted in exception: " + e.getMessage());
e.printStackTrace(System.err);
}
if (!isValidReference(id))
{
- jalview.bin.Console.errPrintln("Ignoring invalid pdb query: '" + id + "'");
+ jalview.bin.Console
+ .errPrintln("Ignoring invalid pdb query: '" + id + "'");
stopQuery();
return null;
}
String database = parseIds(ids, querystring);
if (database == null)
{
- jalview.bin.Console.errPrintln("Invalid Query string : '" + ids + "'");
- jalview.bin.Console.errPrintln("Should be of form 'dbname:q1;q2;q3;q4'");
+ jalview.bin.Console
+ .errPrintln("Invalid Query string : '" + ids + "'");
+ jalview.bin.Console
+ .errPrintln("Should be of form 'dbname:q1;q2;q3;q4'");
return null;
}
"Warning: response code " + responseCode + " for " + url);
} catch (OutOfMemoryError er)
{
- jalview.bin.Console.outPrintln("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
- + ":\n" + ids);
+ jalview.bin.Console.outPrintln("OUT OF MEMORY DOWNLOADING QUERY FROM "
+ + database + ":\n" + ids);
throw er;
} catch (Exception ex)
{
if (!ex.getMessage().startsWith(
"uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
{
- jalview.bin.Console.errPrintln("Unexpected exception when retrieving from "
- + database + "\nQuery was : '" + ids + "'");
+ jalview.bin.Console
+ .errPrintln("Unexpected exception when retrieving from "
+ + database + "\nQuery was : '" + ids + "'");
ex.printStackTrace(System.err);
}
} finally
{
if (!newFrame)
{
- jalview.bin.Console.errPrintln("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+ jalview.bin.Console
+ .errPrintln("MERGE WITH OLD FRAME NOT IMPLEMENTED");
return;
}
// each subjob is an independent alignment for the moment
{
if (cancelJob(rslt))
{
- jalview.bin.Console.errPrintln("Cancelled AACon job: " + rslt);
+ jalview.bin.Console
+ .errPrintln("Cancelled AACon job: " + rslt);
}
else
{
- jalview.bin.Console.errPrintln("FAILED TO CANCEL AACon job: " + rslt);
+ jalview.bin.Console
+ .errPrintln("FAILED TO CANCEL AACon job: " + rslt);
}
} catch (Exception x)
}
else
{
- jalview.bin.Console.errPrintln("Job " + id + " couldn't be cancelled.");
+ jalview.bin.Console
+ .errPrintln("Job " + id + " couldn't be cancelled.");
}
} catch (Exception q)
{
svccategories = registry.getServiceCategories();
// dan test
- // jalview.bin.Console.outPrintln("registry.getServiceCategories: " +
+ // jalview.bin.Console.outPrintln("registry.getServiceCategories: "
+ // +
// svccategories.toString());
}
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Exception whilst trying to get at registry:");
+ jalview.bin.Console.errPrintln(
+ "Exception whilst trying to get at registry:");
ex.printStackTrace();
// if that failed, then we are probably working with a JABAWS1 server.
// in that case, look for each service endpoint
service = Jws2Client.connect(jwsserver, srv);
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Jws2 Discoverer: Problem on " + jwsserver
- + " with service " + srv + ":\n" + e.getMessage());
+ jalview.bin.Console.errPrintln("Jws2 Discoverer: Problem on "
+ + jwsserver + " with service " + srv + ":\n"
+ + e.getMessage());
if (!(e instanceof javax.xml.ws.WebServiceException))
{
e.printStackTrace();
result = false;
} catch (IOException e)
{
- jalview.bin.Console.errPrintln("Error connecting to server: " + server + ": "
- + e.toString());
+ jalview.bin.Console.errPrintln("Error connecting to server: "
+ + server + ": " + e.toString());
result = false;
}
}
List<AlignmentAnnotation> ourAnnot, String typeName,
String calcId, SequenceI dseq, int base, Score scr)
{
- jalview.bin.Console.outPrintln("Creating annotation on dseq:" + dseq.getStart()
- + " base is " + base + " and length=" + dseq.getLength()
- + " == " + scr.getScores().size());
+ jalview.bin.Console.outPrintln("Creating annotation on dseq:"
+ + dseq.getStart() + " base is " + base + " and length="
+ + dseq.getLength() + " == " + scr.getScores().size());
// AlignmentAnnotation annotation = new AlignmentAnnotation(
// scr.getMethod(), typeName, new Annotation[]
// {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
List<AlignmentAnnotation> ourAnnot, String typeName,
String calcId, SequenceI dseq, int base, Score scr)
{
- jalview.bin.Console.outPrintln("Creating annotation on dseq:" + dseq.getStart()
- + " base is " + base + " and length=" + dseq.getLength()
- + " == " + scr.getScores().size());
+ jalview.bin.Console.outPrintln("Creating annotation on dseq:"
+ + dseq.getStart() + " base is " + base + " and length="
+ + dseq.getLength() + " == " + scr.getScores().size());
// AlignmentAnnotation annotation = new AlignmentAnnotation(
// scr.getMethod(), typeName, new Annotation[]
// {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
{
if (getDiscoverer().services != null)
{
- jalview.bin.Console.outPrintln("Changesupport: There are now "
- + getDiscoverer().services.size() + " services");
+ jalview.bin.Console
+ .outPrintln("Changesupport: There are now "
+ + getDiscoverer().services.size()
+ + " services");
int i = 1;
for (Jws2Instance instance : getDiscoverer().services)
{
Option o = options.getArgumentByOptionName(oname);
if (o == null)
{
- jalview.bin.Console.outPrintln("WARN ignoring unsuppoted parameter: " + oname);
+ jalview.bin.Console
+ .outPrintln("WARN ignoring unsuppoted parameter: " + oname);
continue;
}
if (o instanceof Parameter)
}
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Exception when retrieving presets for service "
- + serviceType + " at " + hosturl);
+ jalview.bin.Console
+ .errPrintln("Exception when retrieving presets for service "
+ + serviceType + " at " + hosturl);
}
}
return presets;
: null));
} catch (Exception ex)
{
- jalview.bin.Console.errPrintln("Unexpected exception creating JabaParamStore.");
+ jalview.bin.Console.errPrintln(
+ "Unexpected exception creating JabaParamStore.");
ex.printStackTrace();
}
@Override
public void cancelJob()
{
- jalview.bin.Console.errPrintln("Cannot cancel this job type: " + service);
+ jalview.bin.Console
+ .errPrintln("Cannot cancel this job type: " + service);
}
@Override
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
- jalview.bin.Console.outPrintln(">>> SIFTS File already downloaded for " + pdbId);
+ jalview.bin.Console
+ .outPrintln(">>> SIFTS File already downloaded for " + pdbId);
if (isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
}
}
- // jalview.bin.Console.outPrintln(">> Download ftp url : " + siftsFileFTPURL);
+ // jalview.bin.Console.outPrintln(">> Download ftp url : " +
+ // siftsFileFTPURL);
// long now = System.currentTimeMillis();
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
}
outputStream.close();
inputStream.close();
- // jalview.bin.Console.outPrintln(">>> File downloaded : " + downloadedSiftsFile
+ // jalview.bin.Console.outPrintln(">>> File downloaded : " +
+ // downloadedSiftsFile
// + " took " + (System.currentTimeMillis() - now) + "ms");
return downloadTo;
}
public static String getDownloadUrlFor(String siftFile)
{
- String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile;
- Console.trace("SIFTS URL for "+siftFile+" is "+durl);
+ String durl = SIFTS_SPLIT_FTP_BASE_URL + siftFile.substring(1, 3) + "/"
+ + siftFile;
+ Console.trace("SIFTS URL for " + siftFile + " is " + durl);
return durl;
-
+
}
/**
seq = seq.getDatasetSequence();
}
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
- jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId + ": seq "
- + seq.getName());
+ jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId
+ + ": seq " + seq.getName());
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
if (mapping.isEmpty())
{
- throw new SiftsException("SIFTS mapping failed for "+entityId+" and "+seq.getName());
+ throw new SiftsException("SIFTS mapping failed for " + entityId
+ + " and " + seq.getName());
}
// also construct a mapping object between the seq-coord sys and the PDB
// seq's coord sys
int firstPDBResNum = UNASSIGNED;
for (Segment segment : segments)
{
- // jalview.bin.Console.outPrintln("Mapping segments : " + segment.getSegId() + "\\"s
+ // jalview.bin.Console.outPrintln("Mapping segments : " +
+ // segment.getSegId() + "\\"s
// + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
*/
public Entity getEntityByMostOptimalMatchedId(String chainId)
{
- // jalview.bin.Console.outPrintln("---> advanced greedy entityId matching block
+ // jalview.bin.Console.outPrintln("---> advanced greedy entityId matching
+ // block
// entered..");
List<Entity> entities = siftsEntry.getEntity();
SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
++count;
}
Arrays.sort(sPojo, Collections.reverseOrder());
- // jalview.bin.Console.outPrintln("highest matched entity : " + sPojo[0].entityId);
+ // jalview.bin.Console.outPrintln("highest matched entity : " +
+ // sPojo[0].entityId);
// jalview.bin.Console.outPrintln("highest matched pid : " + sPojo[0].pid);
if (sPojo[0].entityId != null)
}
} catch (IOException e)
{
- jalview.bin.Console.outPrintln("Exception while closing download channel: "
- + e.getMessage());
+ jalview.bin.Console
+ .outPrintln("Exception while closing download channel: "
+ + e.getMessage());
}
try
{
}
} catch (IOException e)
{
- jalview.bin.Console.outPrintln("Exception while deleting download temp file: "
- + e.getMessage());
+ jalview.bin.Console
+ .outPrintln("Exception while deleting download temp file: "
+ + e.getMessage());
}
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="alcodon" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; &lt;attribute
+ * name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "alcodon",
- "alcodMap"
-})
+@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
@XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame {
+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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="thresholdLine" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}annotationElement"
+ * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="label"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="description" type="{http://www.w3.org/2001/XMLSchema}string"
+ * minOccurs="0"/&gt; &lt;element name="thresholdLine"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="contactmatrix"
+ * type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType"
+ * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="property"
+ * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="graphType"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="groupRef"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphGroup"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="scoreOnly"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="score"
+ * type="{http://www.w3.org/2001/XMLSchema}double" /&gt; &lt;attribute
+ * name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="showAllColLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="belowAlignment"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="calcId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "annotationElement",
- "label",
- "description",
- "thresholdLine",
- "contactmatrix",
- "property"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "annotationElement", "label", "description", "thresholdLine",
+ "contactmatrix", "property" })
@XmlRootElement(name = "Annotation")
-public class Annotation {
-
- protected List<AnnotationElement> annotationElement;
- @XmlElement(required = true)
- protected String label;
- protected String description;
- protected Annotation.ThresholdLine thresholdLine;
- protected List<MapOnAMatrixType> contactmatrix;
- protected List<Property> property;
- @XmlAttribute(name = "graph", required = true)
- protected boolean graph;
- @XmlAttribute(name = "graphType")
- protected Integer graphType;
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "groupRef")
- protected String groupRef;
- @XmlAttribute(name = "graphColour")
- protected Integer graphColour;
- @XmlAttribute(name = "graphGroup")
- protected Integer graphGroup;
- @XmlAttribute(name = "graphHeight")
- protected Integer graphHeight;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "scoreOnly")
- protected Boolean scoreOnly;
- @XmlAttribute(name = "score")
- protected Double score;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- @XmlAttribute(name = "centreColLabels")
- protected Boolean centreColLabels;
- @XmlAttribute(name = "scaleColLabels")
- protected Boolean scaleColLabels;
- @XmlAttribute(name = "showAllColLabels")
- protected Boolean showAllColLabels;
- @XmlAttribute(name = "autoCalculated")
- protected Boolean autoCalculated;
- @XmlAttribute(name = "belowAlignment")
- protected Boolean belowAlignment;
- @XmlAttribute(name = "calcId")
- protected String calcId;
-
- /**
- * 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 MapOnAMatrixType }
- *
- *
- */
- public List<MapOnAMatrixType> getContactmatrix() {
- if (contactmatrix == null) {
- contactmatrix = new ArrayList<MapOnAMatrixType>();
- }
- 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;
- }
+public class Annotation
+{
- /**
- * 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;
- }
+ protected List<AnnotationElement> annotationElement;
- /**
- * Gets the value of the scoreOnly property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScoreOnly() {
- if (scoreOnly == null) {
- return false;
- } else {
- return scoreOnly;
- }
- }
+ @XmlElement(required = true)
+ protected String label;
- /**
- * Sets the value of the scoreOnly property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScoreOnly(Boolean value) {
- this.scoreOnly = value;
- }
+ protected String description;
- /**
- * Gets the value of the score property.
- *
- * @return
- * possible object is
- * {@link Double }
- *
- */
- public Double getScore() {
- return score;
- }
+ protected Annotation.ThresholdLine thresholdLine;
+
+ protected List<MapOnAMatrixType> contactmatrix;
+
+ protected List<Property> property;
+
+ @XmlAttribute(name = "graph", required = true)
+ protected boolean graph;
+
+ @XmlAttribute(name = "graphType")
+ protected Integer graphType;
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "groupRef")
+ protected String groupRef;
+
+ @XmlAttribute(name = "graphColour")
+ protected Integer graphColour;
+
+ @XmlAttribute(name = "graphGroup")
+ protected Integer graphGroup;
+
+ @XmlAttribute(name = "graphHeight")
+ protected Integer graphHeight;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "scoreOnly")
+ protected Boolean scoreOnly;
+
+ @XmlAttribute(name = "score")
+ protected Double score;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "centreColLabels")
+ protected Boolean centreColLabels;
+
+ @XmlAttribute(name = "scaleColLabels")
+ protected Boolean scaleColLabels;
+
+ @XmlAttribute(name = "showAllColLabels")
+ protected Boolean showAllColLabels;
+
+ @XmlAttribute(name = "autoCalculated")
+ protected Boolean autoCalculated;
+
+ @XmlAttribute(name = "belowAlignment")
+ protected Boolean belowAlignment;
+
+ @XmlAttribute(name = "calcId")
+ protected String calcId;
+
+ /**
+ * 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 MapOnAMatrixType }
+ *
+ *
+ */
+ public List<MapOnAMatrixType> getContactmatrix()
+ {
+ if (contactmatrix == null)
+ {
+ contactmatrix = new ArrayList<MapOnAMatrixType>();
+ }
+ 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class ThresholdLine
+ {
+
+ @XmlAttribute(name = "label")
+ protected String label;
- /**
- * 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class ThresholdLine {
-
- @XmlAttribute(name = "label")
- protected String label;
- @XmlAttribute(name = "value")
- protected Float value;
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the label property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLabel() {
- return label;
- }
-
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLabel(String value) {
- this.label = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setValue(Float value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
-
- }
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="AnnotationColourScheme"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="AnnotationColourScheme"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="annotation"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="maxColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="predefinedColours"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme {
-
- @XmlAttribute(name = "aboveThreshold")
- protected Integer aboveThreshold;
- @XmlAttribute(name = "annotation")
- protected String annotation;
- @XmlAttribute(name = "minColour")
- protected Integer minColour;
- @XmlAttribute(name = "maxColour")
- protected Integer maxColour;
- @XmlAttribute(name = "colourScheme")
- protected String colourScheme;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "perSequence")
- protected Boolean perSequence;
- @XmlAttribute(name = "predefinedColours")
- protected Boolean predefinedColours;
-
- /**
- * Gets the value of the aboveThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getAboveThreshold() {
- return aboveThreshold;
- }
-
- /**
- * Sets the value of the aboveThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setAboveThreshold(Integer value) {
- this.aboveThreshold = value;
- }
-
- /**
- * Gets the value of the annotation property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotation() {
- return annotation;
- }
-
- /**
- * Sets the value of the annotation property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAnnotation(String value) {
- this.annotation = value;
- }
-
- /**
- * Gets the value of the minColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMinColour() {
- return minColour;
- }
-
- /**
- * Sets the value of the minColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMinColour(Integer value) {
- this.minColour = value;
- }
-
- /**
- * Gets the value of the maxColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMaxColour() {
- return maxColour;
- }
-
- /**
- * Sets the value of the maxColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMaxColour(Integer value) {
- this.maxColour = value;
- }
-
- /**
- * Gets the value of the colourScheme property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColourScheme() {
- return colourScheme;
- }
-
- /**
- * Sets the value of the colourScheme property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColourScheme(String value) {
- this.colourScheme = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the perSequence property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPerSequence() {
- return perSequence;
- }
-
- /**
- * Sets the value of the perSequence property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPerSequence(Boolean value) {
- this.perSequence = value;
- }
-
- /**
- * Gets the value of the predefinedColours property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPredefinedColours() {
- return predefinedColours;
- }
-
- /**
- * Sets the value of the predefinedColours property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPredefinedColours(Boolean value) {
- this.predefinedColours = value;
- }
+public class AnnotationColourScheme
+{
+
+ @XmlAttribute(name = "aboveThreshold")
+ protected Integer aboveThreshold;
+
+ @XmlAttribute(name = "annotation")
+ protected String annotation;
+
+ @XmlAttribute(name = "minColour")
+ protected Integer minColour;
+
+ @XmlAttribute(name = "maxColour")
+ protected Integer maxColour;
+
+ @XmlAttribute(name = "colourScheme")
+ protected String colourScheme;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "perSequence")
+ protected Boolean perSequence;
+
+ @XmlAttribute(name = "predefinedColours")
+ protected Boolean predefinedColours;
+
+ /**
+ * Gets the value of the aboveThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getAboveThreshold()
+ {
+ return aboveThreshold;
+ }
+
+ /**
+ * Sets the value of the aboveThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setAboveThreshold(Integer value)
+ {
+ this.aboveThreshold = value;
+ }
+
+ /**
+ * Gets the value of the annotation property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAnnotation()
+ {
+ return annotation;
+ }
+
+ /**
+ * Sets the value of the annotation property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAnnotation(String value)
+ {
+ this.annotation = value;
+ }
+
+ /**
+ * Gets the value of the minColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMinColour()
+ {
+ return minColour;
+ }
+
+ /**
+ * Sets the value of the minColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMinColour(Integer value)
+ {
+ this.minColour = value;
+ }
+
+ /**
+ * Gets the value of the maxColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMaxColour()
+ {
+ return maxColour;
+ }
+
+ /**
+ * Sets the value of the maxColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMaxColour(Integer value)
+ {
+ this.maxColour = value;
+ }
+
+ /**
+ * Gets the value of the colourScheme property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColourScheme()
+ {
+ return colourScheme;
+ }
+
+ /**
+ * Sets the value of the colourScheme property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColourScheme(String value)
+ {
+ this.colourScheme = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the perSequence property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPerSequence()
+ {
+ return perSequence;
+ }
+
+ /**
+ * Sets the value of the perSequence property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPerSequence(Boolean value)
+ {
+ this.perSequence = value;
+ }
+
+ /**
+ * Gets the value of the predefinedColours property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPredefinedColours()
+ {
+ return predefinedColours;
+ }
+
+ /**
+ * Sets the value of the predefinedColours property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPredefinedColours(Boolean value)
+ {
+ this.predefinedColours = value;
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="secondaryStructure" minOccurs="0"&gt;
- * &lt;simpleType&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;length value="1"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * &lt;/element&gt;
- * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="displayCharacter"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="secondaryStructure" minOccurs="0"&gt;
+ * &lt;simpleType&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;length
+ * value="1"/&gt; &lt;/restriction&gt; &lt;/simpleType&gt;
+ * &lt;/element&gt; &lt;element name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="position" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "displayCharacter",
- "description",
- "secondaryStructure",
- "value"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "displayCharacter", "description", "secondaryStructure", "value" })
@XmlRootElement(name = "annotationElement")
-public class AnnotationElement {
-
- protected String displayCharacter;
- protected String description;
- protected String secondaryStructure;
- protected Float value;
- @XmlAttribute(name = "position", required = true)
- protected int position;
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the displayCharacter property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDisplayCharacter() {
- return displayCharacter;
- }
-
- /**
- * Sets the value of the displayCharacter property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDisplayCharacter(String value) {
- this.displayCharacter = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSecondaryStructure() {
- return secondaryStructure;
- }
-
- /**
- * Sets the value of the secondaryStructure property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSecondaryStructure(String value) {
- this.secondaryStructure = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setValue(Float value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- */
- public int getPosition() {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- */
- public void setPosition(int value) {
- this.position = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
+public class AnnotationElement
+{
+
+ protected String displayCharacter;
+
+ protected String description;
+
+ protected String secondaryStructure;
+
+ protected Float value;
+
+ @XmlAttribute(name = "position", required = true)
+ protected int position;
+
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the displayCharacter property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDisplayCharacter()
+ {
+ return displayCharacter;
+ }
+
+ /**
+ * Sets the value of the displayCharacter property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDisplayCharacter(String value)
+ {
+ this.displayCharacter = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSecondaryStructure()
+ {
+ return secondaryStructure;
+ }
+
+ /**
+ * Sets the value of the secondaryStructure property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSecondaryStructure(String value)
+ {
+ this.secondaryStructure = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setValue(Float value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ */
+ public int getPosition()
+ {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ */
+ public void setPosition(int value)
+ {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="DoubleMatrix"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
- * &lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="DoubleMatrix"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="row"
+ * type="{www.jalview.org}DoubleVector" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="D"
+ * type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt; &lt;element
+ * name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="rows"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
- "row",
- "d",
- "e"
-})
-public class DoubleMatrix {
-
- protected List<DoubleVector> row;
- @XmlElement(name = "D")
- protected DoubleVector d;
- @XmlElement(name = "E")
- protected DoubleVector e;
- @XmlAttribute(name = "rows")
- protected Integer rows;
- @XmlAttribute(name = "columns")
- protected Integer columns;
-
- /**
- * Gets the value of the row property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the row property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getRow().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DoubleVector }
- *
- *
- */
- public List<DoubleVector> getRow() {
- if (row == null) {
- row = new ArrayList<DoubleVector>();
- }
- 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="DoubleVector"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="DoubleVector"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="v"
+ * type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
- "v"
-})
-public class DoubleVector {
+@XmlType(
+ name = "DoubleVector",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "v" })
+public class DoubleVector
+{
- @XmlElement(type = Double.class)
- protected List<Double> v;
+ @XmlElement(type = Double.class)
+ protected List<Double> v;
- /**
- * Gets the value of the v property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the v property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getV().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Double }
- *
- *
- */
- public List<Double> getV() {
- if (v == null) {
- v = new ArrayList<Double>();
- }
- 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="feature"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="feature"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="otherData"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="key2"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="begin" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="status"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
- "otherData"
-})
-public class Feature {
-
- protected List<Feature.OtherData> otherData;
- @XmlAttribute(name = "begin", required = true)
- protected int begin;
- @XmlAttribute(name = "end", required = true)
- protected int end;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "description")
- protected String description;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "featureGroup")
- protected String featureGroup;
- @XmlAttribute(name = "score")
- protected Float score;
-
- /**
- * Gets the value of the otherData property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the otherData property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getOtherData().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Feature.OtherData }
- *
- *
- */
- public List<Feature.OtherData> getOtherData() {
- if (otherData == null) {
- otherData = new ArrayList<Feature.OtherData>();
- }
- 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="key2"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class OtherData
+ {
+
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+
+ @XmlAttribute(name = "key2")
+ protected String key2;
+
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
/**
- * Gets the value of the 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="FeatureMatcher"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="FeatureMatcher"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="condition"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="by"
+ * type="{www.jalview.org/colours}FilterBy" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
- "attributeName",
- "condition",
- "value"
-})
-public class FeatureMatcher {
+@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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="FeatureMatcherSet"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;choice&gt;
- * &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/&gt;
- * &lt;element name="compoundMatcher"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/choice&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="FeatureMatcherSet"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;choice&gt; &lt;element name="matchCondition"
+ * type="{www.jalview.org/colours}FeatureMatcher"/&gt; &lt;element
+ * name="compoundMatcher"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
+ * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute name="and"
+ * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;/choice&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
- "matchCondition",
- "compoundMatcher"
-})
-public class FeatureMatcherSet {
-
- @XmlElement(namespace = "")
- protected FeatureMatcher matchCondition;
- @XmlElement(namespace = "")
- protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+@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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
+ * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "matcherSet" })
+ public static class CompoundMatcher
+ {
+
+ @XmlElement(namespace = "", required = true)
+ protected List<FeatureMatcherSet> matcherSet;
+
+ @XmlAttribute(name = "and", required = true)
+ protected boolean and;
/**
- * Gets the value of the 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>The following schema fragment specifies the expected content contained within this class.
- * <pre>
- * &lt;simpleType name="FilterBy"&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;enumeration value="byLabel"/&gt;
- * &lt;enumeration value="byScore"/&gt;
- * &lt;enumeration value="byAttribute"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * </pre>
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class. <pre> &lt;simpleType
+ * name="FilterBy"&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
+ * value="byLabel"/&gt; &lt;enumeration value="byScore"/&gt;
+ * &lt;enumeration value="byAttribute"/&gt; &lt;/restriction&gt;
+ * &lt;/simpleType&gt; </pre>
*
*/
@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum FilterBy {
-
- @XmlEnumValue("byLabel")
- BY_LABEL("byLabel"),
- @XmlEnumValue("byScore")
- BY_SCORE("byScore"),
- @XmlEnumValue("byAttribute")
- BY_ATTRIBUTE("byAttribute");
- private final String value;
-
- FilterBy(String v) {
- value = v;
- }
-
- public 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 enum FilterBy
+{
+
+ @XmlEnumValue("byLabel")
+ BY_LABEL("byLabel"), @XmlEnumValue("byScore")
+ BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
+ BY_ATTRIBUTE("byAttribute");
+
+ private final String value;
+
+ FilterBy(String v)
+ {
+ value = v;
+ }
+
+ public String value()
+ {
+ return value;
+ }
+
+ public static FilterBy fromValue(String v)
+ {
+ for (FilterBy c : FilterBy.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="JalviewModel"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
- * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
- * &lt;sequence&gt;
- * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
- * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="overview" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt;
- * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="FeatureSettings" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="JalviewModel"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="creationDate"
+ * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; &lt;element
+ * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="vamsasModel"
+ * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
+ * &lt;sequence&gt; &lt;element name="JSeq" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="features"
+ * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
+ * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;simpleContent&gt; &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/extension&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="hiddenSequences"
+ * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="rnaViewer" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="secondaryStructure"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="hidden"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="seq"
+ * type="{http://www.w3.org/2001/XMLSchema}string"
+ * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="start"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="showUnconserved"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="true" /&gt; &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="AnnotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
+ * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="autoUpdate" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="overview" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="residueColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="hiddenColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="pidSelected"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="showBoxes"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="renderGaps"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="showNPfeatureTooltip"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="followHighlight"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="showGroupConservation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charWidth"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="idWidthManuallyAdjusted"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="true" /&gt; &lt;attribute name="viewName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="gatheredViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; &lt;attribute
+ * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="UserColourScheme"
+ * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt; &lt;element name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="fontName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="markUnlinked"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="columnReference"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="sequencePoint"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;attribute name="sequenceRef"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="seqPointMax"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="pcaData"
+ * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="xDim"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="bgColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="FeatureSettings" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="setting" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
+ * default="Min" /&gt; &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;/sequence&gt; &lt;/sequence&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
- "creationDate",
- "version",
- "vamsasModel",
- "jSeq",
- "jGroup",
- "viewport",
- "userColours",
- "tree",
- "pcaViewer",
- "featureSettings"
-})
-public class JalviewModel {
-
- @XmlElement(required = true)
- @XmlSchemaType(name = "dateTime")
- protected XMLGregorianCalendar creationDate;
- @XmlElement(required = true)
- protected String version;
- @XmlElement(required = true)
- protected VAMSAS vamsasModel;
- @XmlElement(name = "JSeq")
- protected List<JalviewModel.JSeq> jSeq;
- @XmlElement(name = "JGroup")
- protected List<JalviewModel.JGroup> jGroup;
- @XmlElement(name = "Viewport")
- protected List<JalviewModel.Viewport> viewport;
- @XmlElement(name = "UserColours")
- protected List<JalviewModel.UserColours> userColours;
- protected List<JalviewModel.Tree> tree;
- @XmlElement(name = "PcaViewer")
- protected List<JalviewModel.PcaViewer> pcaViewer;
- @XmlElement(name = "FeatureSettings")
- protected JalviewModel.FeatureSettings featureSettings;
-
- /**
- * Gets the value of the creationDate property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreationDate() {
- return creationDate;
- }
-
- /**
- * Sets the value of the creationDate property.
+@XmlType(
+ name = "JalviewModel",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+ "userColours", "tree", "pcaViewer", "featureSettings" })
+public class JalviewModel
+{
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+
+ @XmlElement(required = true)
+ protected String version;
+
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModel.JSeq> jSeq;
+
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModel.JGroup> jGroup;
+
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModel.Viewport> viewport;
+
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModel.UserColours> userColours;
+
+ protected List<JalviewModel.Tree> tree;
+
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
+
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModel.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate()
+ {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreationDate(XMLGregorianCalendar value)
+ {
+ this.creationDate = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the vamsasModel property.
+ *
+ * @return possible object is {@link VAMSAS }
+ *
+ */
+ public VAMSAS getVamsasModel()
+ {
+ return vamsasModel;
+ }
+
+ /**
+ * Sets the value of the vamsasModel property.
+ *
+ * @param value
+ * allowed object is {@link VAMSAS }
+ *
+ */
+ public void setVamsasModel(VAMSAS value)
+ {
+ this.vamsasModel = value;
+ }
+
+ /**
+ * Gets the value of the jSeq property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the jSeq property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getJSeq().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq> getJSeq()
+ {
+ if (jSeq == null)
+ {
+ jSeq = new ArrayList<JalviewModel.JSeq>();
+ }
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the jGroup property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getJGroup().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
+ *
+ *
+ */
+ public List<JalviewModel.JGroup> getJGroup()
+ {
+ if (jGroup == null)
+ {
+ jGroup = new ArrayList<JalviewModel.JGroup>();
+ }
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the viewport property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getViewport().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport> getViewport()
+ {
+ if (viewport == null)
+ {
+ viewport = new ArrayList<JalviewModel.Viewport>();
+ }
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the userColours property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getUserColours().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
+ *
+ *
+ */
+ public List<JalviewModel.UserColours> getUserColours()
+ {
+ if (userColours == null)
+ {
+ userColours = new ArrayList<JalviewModel.UserColours>();
+ }
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the tree property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getTree().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
+ *
+ *
+ */
+ public List<JalviewModel.Tree> getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList<JalviewModel.Tree>();
+ }
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the pcaViewer property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the pcaViewer property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getPcaViewer().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer> getPcaViewer()
+ {
+ if (pcaViewer == null)
+ {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+ }
+ return this.pcaViewer;
+ }
+
+ /**
+ * Gets the value of the featureSettings property.
+ *
+ * @return possible object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings getFeatureSettings()
+ {
+ return featureSettings;
+ }
+
+ /**
+ * Sets the value of the featureSettings property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModel.FeatureSettings value)
+ {
+ this.featureSettings = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="setting"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour"
+ * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "setting", "group" })
+ public static class FeatureSettings
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Setting> setting;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Group> group;
+
+ /**
+ * Gets the value of the setting property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the setting property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSetting().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Setting }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Setting> getSetting()
+ {
+ if (setting == null)
+ {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
+ }
+
+ /**
+ * Gets the value of the group property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the group property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getGroup().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Group }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Group> getGroup()
+ {
+ if (group == null)
+ {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
+ * default="Min" /&gt; &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+ public static class Setting
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ @XmlAttribute(name = "order")
+ protected Float order;
+
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+
+ @XmlAttribute(name = "max")
+ protected Float max;
+
+ @XmlAttribute(name = "min")
+ protected Float min;
+
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p> This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the returned
+ * list will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAttributeName().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return possible object is {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value)
+ {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getOrder()
+ {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setOrder(Float value)
+ {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMincolour()
+ {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value)
+ {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
+ }
+ else
+ {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getThreshstate()
+ {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value)
+ {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMax(Float value)
+ {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMin()
+ {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMin(Float value)
+ {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel()
+ {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value)
+ {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale()
+ {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value)
+ {
+ this.autoScale = value;
+ }
+
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="seq"
+ * type="{http://www.w3.org/2001/XMLSchema}string"
+ * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="start"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="displayText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="ignoreGapsinConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+ public static class JGroup
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "colour")
+ protected String colour;
+
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the seq property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the seq property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSeq().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
*
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
*/
- public void setCreationDate(XMLGregorianCalendar value) {
- this.creationDate = value;
+ public List<String> getSeq()
+ {
+ if (seq == null)
+ {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
}
/**
- * Gets the value of the version property.
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getVersion() {
- return version;
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
}
/**
- * Sets the value of the version property.
+ * Sets the value of the annotationColours property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link AnnotationColourScheme }
+ *
*/
- public void setVersion(String value) {
- this.version = value;
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
}
/**
- * Gets the value of the vamsasModel property.
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link VAMSAS }
- *
*/
- public VAMSAS getVamsasModel() {
- return vamsasModel;
+ public Integer getStart()
+ {
+ return start;
}
/**
- * Sets the value of the vamsasModel property.
+ * Sets the value of the start property.
*
* @param value
- * allowed object is
- * {@link VAMSAS }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setVamsasModel(VAMSAS value) {
- this.vamsasModel = value;
+ public void setStart(Integer value)
+ {
+ this.start = value;
}
/**
- * Gets the value of the jSeq property.
+ * Gets the value of the end property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make 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.
+ * @return possible object is {@link Integer }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getJSeq().add(newItem);
- * </pre>
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the name property.
*
+ * @return possible object is {@link String }
*
*/
- public List<JalviewModel.JSeq> getJSeq() {
- if (jSeq == null) {
- jSeq = new ArrayList<JalviewModel.JSeq>();
- }
- return this.jSeq;
+ public String getName()
+ {
+ return name;
}
/**
- * Gets the value of the jGroup property.
+ * Sets 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 jGroup property.
+ * @param value
+ * allowed object is {@link String }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getJGroup().add(newItem);
- * </pre>
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
*
+ * @return possible object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JGroup }
+ */
+ public String getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<JalviewModel.JGroup> getJGroup() {
- if (jGroup == null) {
- jGroup = new ArrayList<JalviewModel.JGroup>();
- }
- return this.jGroup;
+ public void setColour(String value)
+ {
+ this.colour = value;
}
/**
- * Gets the value of the viewport property.
+ * Gets the value of the consThreshold property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make 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.
+ * @return possible object is {@link Integer }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getViewport().add(newItem);
- * </pre>
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
+
+ /**
+ * Sets the value of the consThreshold property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport }
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
+
+ /**
+ * Gets the value of the pidThreshold property.
*
+ * @return possible object is {@link Integer }
*
*/
- public List<JalviewModel.Viewport> getViewport() {
- if (viewport == null) {
- viewport = new ArrayList<JalviewModel.Viewport>();
- }
- return this.viewport;
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
}
/**
- * Gets the value of the userColours property.
+ * Sets the value of the pidThreshold property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make 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.
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getUserColours().add(newItem);
- * </pre>
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
+
+ /**
+ * Gets the value of the outlineColour property.
*
+ * @return possible object is {@link Integer }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.UserColours }
+ */
+ public Integer getOutlineColour()
+ {
+ return outlineColour;
+ }
+
+ /**
+ * Sets the value of the outlineColour property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- public List<JalviewModel.UserColours> getUserColours() {
- if (userColours == null) {
- userColours = new ArrayList<JalviewModel.UserColours>();
- }
- return this.userColours;
+ public void setOutlineColour(Integer value)
+ {
+ this.outlineColour = value;
}
/**
- * Gets the value of the tree property.
+ * Gets the value of the displayBoxes property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make 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 Boolean }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTree().add(newItem);
- * </pre>
+ */
+ public Boolean isDisplayBoxes()
+ {
+ return displayBoxes;
+ }
+
+ /**
+ * Sets the value of the displayBoxes property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Tree }
+ */
+ public void setDisplayBoxes(Boolean value)
+ {
+ this.displayBoxes = value;
+ }
+
+ /**
+ * Gets the value of the displayText property.
*
+ * @return possible object is {@link Boolean }
*
*/
- public List<JalviewModel.Tree> getTree() {
- if (tree == null) {
- tree = new ArrayList<JalviewModel.Tree>();
- }
- return this.tree;
+ public Boolean isDisplayText()
+ {
+ return displayText;
}
/**
- * Gets the value of the pcaViewer property.
+ * Sets the value of the displayText property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make 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 Boolean }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getPcaViewer().add(newItem);
- * </pre>
+ */
+ public void setDisplayText(Boolean value)
+ {
+ this.displayText = value;
+ }
+
+ /**
+ * Gets the value of the colourText property.
*
+ * @return possible object is {@link Boolean }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer }
+ */
+ public Boolean isColourText()
+ {
+ return colourText;
+ }
+
+ /**
+ * Sets the value of the colourText property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
*/
- public List<JalviewModel.PcaViewer> getPcaViewer() {
- if (pcaViewer == null) {
- pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
- }
- return this.pcaViewer;
+ public void setColourText(Boolean value)
+ {
+ this.colourText = value;
}
/**
- * Gets the value of the featureSettings property.
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link JalviewModel.FeatureSettings }
- *
*/
- public JalviewModel.FeatureSettings getFeatureSettings() {
- return featureSettings;
+ public Integer getTextCol1()
+ {
+ return textCol1;
}
/**
- * Sets the value of the featureSettings property.
+ * Sets the value of the textCol1 property.
*
* @param value
- * allowed object is
- * {@link JalviewModel.FeatureSettings }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setFeatureSettings(JalviewModel.FeatureSettings value) {
- this.featureSettings = value;
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
}
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
+
+ /**
+ * Gets the value of the textColThreshold property.
*
+ * @return possible object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "setting",
- "group"
- })
- public static class FeatureSettings {
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- @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 textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = 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 showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowUnconserved()
+ {
+ return showUnconserved;
+ }
- /**
- * 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 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;
+ }
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Group {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
+ /**
+ * 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;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "attributeName",
- "matcherSet"
- })
- public static class Setting {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<String> attributeName;
- @XmlElement(namespace = "www.jalview.org")
- protected FeatureMatcherSet matcherSet;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "colour", required = true)
- protected int colour;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
- @XmlAttribute(name = "order")
- protected Float order;
- @XmlAttribute(name = "mincolour")
- protected Integer mincolour;
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "threshstate")
- protected Integer threshstate;
- @XmlAttribute(name = "max")
- protected Float max;
- @XmlAttribute(name = "min")
- protected Float min;
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return
- * possible object is
- * {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet() {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value) {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- */
- public int getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- */
- public void setColour(int value) {
- this.colour = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
-
- /**
- * Gets the value of the order property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getOrder() {
- return order;
- }
-
- /**
- * Sets the value of the order property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setOrder(Float value) {
- this.order = value;
- }
-
- /**
- * Gets the value of the mincolour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMincolour() {
- return mincolour;
- }
-
- /**
- * Sets the value of the mincolour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMincolour(Integer value) {
- this.mincolour = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return
- * possible object is
- * {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour() {
- if (noValueColour == null) {
- return NoValueColour.MIN;
- } else {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is
- * {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value) {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the threshstate property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getThreshstate() {
- return threshstate;
- }
-
- /**
- * Sets the value of the threshstate property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setThreshstate(Integer value) {
- this.threshstate = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMax(Float value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMin() {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMin(Float value) {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourByLabel() {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value) {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isAutoScale() {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value) {
- this.autoScale = value;
- }
+ /**
+ * 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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
- * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @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 setId(String value)
+ {
+ this.id = 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;
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="features"
+ * type="{www.jalview.org}feature" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="pdbids" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;extension
+ * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;simpleContent&gt; &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="true" /&gt; &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/extension&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="hiddenSequences"
+ * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="rnaViewer"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="secondaryStructure"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="hidden"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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 annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ /**
+ * 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 annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = 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 start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
+ /**
+ * 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 start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = 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 end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
- /**
- * 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 colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart()
+ {
+ return start;
+ }
- /**
- * 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 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt; &lt;element name="structureState"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;simpleContent&gt; &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/extension&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "structureState" })
+ public static class Pdbids extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p> This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the returned
+ * list will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the structureState property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getStructureState().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
+ {
+ if (structureState == null)
+ {
+ structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+ }
+ return this.structureState;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;simpleContent&gt;
+ * &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
+ * /&gt; &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
+ * /&gt; &lt;attribute name="type"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class StructureState
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
/**
- * Gets the value of the colour property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getColour() {
- return colour;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setColour(String value) {
- this.colour = value;
+ public void setValue(String value)
+ {
+ this.value = value;
}
/**
- * Gets the value of the consThreshold property.
+ * Gets the value of the visible property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getConsThreshold() {
- return consThreshold;
+ public Boolean isVisible()
+ {
+ return visible;
}
/**
- * Sets the value of the consThreshold property.
+ * Sets the value of the visible property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
}
/**
- * Gets the value of the pidThreshold property.
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getPidThreshold() {
- return pidThreshold;
+ public String getViewId()
+ {
+ return viewId;
}
/**
- * Sets the value of the pidThreshold property.
+ * Sets the value of the viewId property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
+ public void setViewId(String value)
+ {
+ this.viewId = value;
}
/**
- * Gets the value of the outlineColour property.
+ * Gets the value of the alignwithAlignPanel 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 }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setOutlineColour(Integer value) {
- this.outlineColour = value;
+ public void setAlignwithAlignPanel(Boolean value)
+ {
+ this.alignwithAlignPanel = value;
}
/**
- * Gets the value of the displayBoxes property.
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayBoxes() {
- return displayBoxes;
+ public boolean isColourwithAlignPanel()
+ {
+ if (colourwithAlignPanel == null)
+ {
+ return false;
+ }
+ else
+ {
+ return colourwithAlignPanel;
+ }
}
/**
- * Sets the value of the displayBoxes property.
+ * Sets the value of the colourwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setDisplayBoxes(Boolean value) {
- this.displayBoxes = value;
+ public void setColourwithAlignPanel(Boolean value)
+ {
+ this.colourwithAlignPanel = value;
}
/**
- * Gets the value of the displayText property.
+ * Gets the value of the colourByJmol property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayText() {
- return displayText;
+ public boolean isColourByJmol()
+ {
+ if (colourByJmol == null)
+ {
+ return true;
+ }
+ else
+ {
+ return colourByJmol;
+ }
}
/**
- * Sets the value of the displayText property.
+ * Sets the value of the colourByJmol property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setDisplayText(Boolean value) {
- this.displayText = value;
+ public void setColourByJmol(Boolean value)
+ {
+ this.colourByJmol = value;
}
/**
- * Gets the value of the colourText property.
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isColourText() {
- return colourText;
+ public String getType()
+ {
+ return type;
}
/**
- * Sets the value of the colourText property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setColourText(Boolean value) {
- this.colourText = value;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the textCol1 property.
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol1() {
- return textCol1;
+ public Integer getWidth()
+ {
+ return width;
}
/**
- * Sets the value of the textCol1 property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
+ public void setWidth(Integer value)
+ {
+ this.width = value;
}
/**
- * Gets the value of the textCol2 property.
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol2() {
- return textCol2;
+ public Integer getHeight()
+ {
+ return height;
}
/**
- * Sets the value of the textCol2 property.
+ * Sets the value of the height property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
+ public void setHeight(Integer value)
+ {
+ this.height = value;
}
/**
- * Gets the value of the textColThreshold property.
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextColThreshold() {
- return textColThreshold;
+ public Integer getXpos()
+ {
+ return xpos;
}
/**
- * Sets the value of the textColThreshold property.
+ * Sets the value of the xpos property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
}
/**
- * Gets the value of the showUnconserved property.
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowUnconserved() {
- return showUnconserved;
+ public Integer getYpos()
+ {
+ return ypos;
}
/**
- * Sets the value of the showUnconserved property.
+ * Sets the value of the ypos property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="secondaryStructure"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "secondaryStructure" })
+ public static class RnaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p> This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the returned
+ * list will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the secondaryStructure
+ * property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSecondaryStructure().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
+ {
+ if (secondaryStructure == null)
+ {
+ secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewId()
+ {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewId(String value)
+ {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getDividerLocation()
+ {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value)
+ {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getSelectedRna()
+ {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value)
+ {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure
+ {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
+
/**
- * Gets the value of the ignoreGapsinConsensus property.
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
+ public String getTitle()
+ {
+ return title;
}
/**
- * Sets the value of the ignoreGapsinConsensus property.
+ * Sets the value of the title property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
+ public void setTitle(String value)
+ {
+ this.title = value;
}
/**
- * Gets the value of the showConsensusHistogram property.
+ * Gets the value of the annotationId 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 getAnnotationId()
+ {
+ return annotationId;
}
/**
- * Sets the value of the showConsensusHistogram property.
+ * Sets the value of the annotationId property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
+ public void setAnnotationId(String value)
+ {
+ this.annotationId = value;
}
/**
- * Gets the value of the showSequenceLogo property.
+ * Gets the value of the gapped property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
+ public Boolean isGapped()
+ {
+ return gapped;
}
/**
- * Sets the value of the showSequenceLogo property.
+ * Sets the value of the gapped property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
+ public void setGapped(Boolean value)
+ {
+ this.gapped = value;
}
/**
- * Gets the value of the normaliseSequenceLogo property.
+ * Gets the value of the viewerState property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
+ public String getViewerState()
+ {
+ return viewerState;
}
/**
- * Sets the value of the normaliseSequenceLogo property.
+ * Sets the value of the viewerState property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
-
- /**
- * Gets the value of the id property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public void setViewerState(String value)
+ {
+ this.viewerState = value;
}
- /**
- * 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="sequencePoint"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;attribute
+ * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="pcaData"
+ * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="xDim"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="bgColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the sequencePoint property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make 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 }
*
*
*/
- @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;
- }
+ public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
+ {
+ if (sequencePoint == null)
+ {
+ sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+ }
+ return this.sequencePoint;
+ }
- /**
- * 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 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 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 seqPointMin property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
+ {
+ return seqPointMin;
+ }
- /**
- * 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;
- }
+ /**
+ * 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 colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
+ /**
+ * 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 colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
+ /**
+ * Sets the value of the seqPointMax property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
+ {
+ this.seqPointMax = value;
+ }
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart() {
- return start;
- }
+ /**
+ * Gets the value of the pcaData property.
+ *
+ * @return possible object is {@link PcaDataType }
+ *
+ */
+ public PcaDataType getPcaData()
+ {
+ return pcaData;
+ }
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value) {
- this.start = value;
- }
+ /**
+ * Sets the value of the pcaData property.
+ *
+ * @param value
+ * allowed object is {@link PcaDataType }
+ *
+ */
+ public void setPcaData(PcaDataType value)
+ {
+ this.pcaData = value;
+ }
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value) {
- this.end = 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 id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the scoreModelName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScoreModelName()
+ {
+ return scoreModelName;
+ }
- /**
- * 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 scoreModelName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScoreModelName(String value)
+ {
+ this.scoreModelName = value;
+ }
- /**
- * Gets the value of the hidden property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isHidden() {
- return hidden;
- }
+ /**
+ * Gets the value of the xDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXDim()
+ {
+ return xDim;
+ }
- /**
- * Sets the value of the hidden property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setHidden(Boolean value) {
- this.hidden = value;
- }
+ /**
+ * 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 viewreference property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isViewreference() {
- return viewreference;
- }
+ /**
+ * Gets the value of the yDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYDim()
+ {
+ return yDim;
+ }
- /**
- * Sets the value of the viewreference property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setViewreference(Boolean value) {
- this.viewreference = 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "structureState"
- })
- public static class Pdbids
- extends Pdbentry
- {
+ /**
+ * Sets the value of the zDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setZDim(Integer value)
+ {
+ this.zDim = value;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the structureState property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getStructureState().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
- if (structureState == null) {
- structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class StructureState {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isVisible() {
- return visible;
- }
-
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setVisible(Boolean value) {
- this.visible = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the alignwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isAlignwithAlignPanel() {
- if (alignwithAlignPanel == null) {
- return true;
- } else {
- return alignwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the alignwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAlignwithAlignPanel(Boolean value) {
- this.alignwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourwithAlignPanel() {
- if (colourwithAlignPanel == null) {
- return false;
- } else {
- return colourwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the colourwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourwithAlignPanel(Boolean value) {
- this.colourwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourByJmol property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourByJmol() {
- if (colourByJmol == null) {
- return true;
- } else {
- return colourByJmol;
- }
- }
-
- /**
- * Sets the value of the colourByJmol property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByJmol(Boolean value) {
- this.colourByJmol = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getBgColour()
+ {
+ return bgColour;
+ }
- }
+ /**
+ * 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "secondaryStructure"
- })
- public static class RnaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSecondaryStructure().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
- if (secondaryStructure == null) {
- secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the dividerLocation property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getDividerLocation() {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setDividerLocation(Integer value) {
- this.dividerLocation = value;
- }
-
- /**
- * Gets the value of the selectedRna property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getSelectedRna() {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setSelectedRna(Integer value) {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure {
-
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the annotationId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotationId() {
- return annotationId;
- }
-
- /**
- * Sets the value of the annotationId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAnnotationId(String value) {
- this.annotationId = value;
- }
-
- /**
- * Gets the value of the gapped property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGapped() {
- return gapped;
- }
-
- /**
- * Sets the value of the gapped property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGapped(Boolean value) {
- this.gapped = value;
- }
-
- /**
- * Gets the value of the viewerState property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewerState() {
- return viewerState;
- }
-
- /**
- * Sets the value of the viewerState property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewerState(String value) {
- this.viewerState = value;
- }
-
- }
+ /**
+ * 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;
+ }
+ /**
+ * 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 linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews()
+ {
+ return linkToAllViews;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the linkToAllViews property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
+
+ /**
+ * Gets the value of the includeGaps property.
*
+ * @return possible object is {@link Boolean }
*
*/
- @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;
- }
+ public Boolean isIncludeGaps()
+ {
+ return includeGaps;
+ }
- /**
- * Gets the value of the scoreModelName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScoreModelName() {
- return scoreModelName;
- }
+ /**
+ * 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 scoreModelName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScoreModelName(String value) {
- this.scoreModelName = value;
- }
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps()
+ {
+ return matchGaps;
+ }
- /**
- * Gets the value of the xDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXDim() {
- return xDim;
- }
+ /**
+ * 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 xDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXDim(Integer value) {
- this.xDim = value;
- }
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns()
+ {
+ return includeGappedColumns;
+ }
- /**
- * Gets the value of the yDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYDim() {
- return yDim;
- }
+ /**
+ * 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 yDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYDim(Integer value) {
- this.yDim = value;
- }
+ /**
+ * Gets the value of the denominateByShortestLength property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDenominateByShortestLength()
+ {
+ return denominateByShortestLength;
+ }
- /**
- * Gets the value of the zDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getZDim() {
- return zDim;
- }
+ /**
+ * Sets the value of the denominateByShortestLength property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDenominateByShortestLength(Boolean value)
+ {
+ this.denominateByShortestLength = value;
+ }
- /**
- * Sets the value of the zDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setZDim(Integer value) {
- this.zDim = value;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getBgColour() {
- return bgColour;
- }
+ /**
+ * 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 bgColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setBgColour(Integer value) {
- this.bgColour = value;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Gets the value of the scaleFactor property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getScaleFactor() {
- return scaleFactor;
- }
+ /**
+ * 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 scaleFactor property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setScaleFactor(Float value) {
- this.scaleFactor = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Gets the value of the showLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowLabels() {
- return showLabels;
- }
+ /**
+ * 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 showLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowLabels(Boolean value) {
- this.showLabels = value;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isLinkToAllViews() {
- return linkToAllViews;
- }
+ /**
+ * 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 linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class 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 includeGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGaps() {
- return includeGaps;
- }
+ }
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the matchGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMatchGaps() {
- return matchGaps;
- }
+ }
- /**
- * Sets the value of the matchGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class 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 includeGappedColumns property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
- }
+ }
- /**
- * Sets the value of the includeGappedColumns property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;attribute
+ * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint
+ {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceRef(String value)
+ {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
+ * minOccurs="0"&gt; &lt;element name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="showDistances"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="columnWise"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="columnReference"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "title", "newick" })
+ public static class Tree
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+
+ @XmlAttribute(name = "columnWise")
+ protected Boolean columnWise;
+
+ @XmlAttribute(name = "columnReference")
+ protected String columnReference;
+
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * 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 title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNewick()
+ {
+ return newick;
+ }
- /**
- * 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 newick property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNewick(String value)
+ {
+ this.newick = value;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * 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 fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * 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 fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Axis {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = 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;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMax {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap()
+ {
+ return showBootstrap;
+ }
- }
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value)
+ {
+ this.showBootstrap = value;
+ }
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances()
+ {
+ return showDistances;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMin {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value)
+ {
+ this.showDistances = value;
+ }
- }
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked()
+ {
+ return markUnlinked;
+ }
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value)
+ {
+ this.markUnlinked = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequencePoint {
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceRef() {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceRef(String value) {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * 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;
+ }
+ /**
+ * 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;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the columnWise property.
+ *
+ * @return possible object is {@link Boolean }
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt;
- * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public boolean isColumnWise()
+ {
+ if (columnWise == null)
+ {
+ return false;
+ }
+ else
+ {
+ return columnWise;
+ }
+ }
+
+ /**
+ * Sets the value of the columnWise property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "newick"
- })
- public static class Tree {
+ public void setColumnWise(Boolean value)
+ {
+ this.columnWise = value;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- @XmlAttribute(name = "columnWise")
- protected Boolean columnWise;
- @XmlAttribute(name = "columnReference")
- protected String columnReference;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * Gets the value of the columnReference property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColumnReference()
+ {
+ return columnReference;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * Sets the value of the columnReference property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColumnReference(String value)
+ {
+ this.columnReference = 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 id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Gets the value of the newick property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNewick() {
- return newick;
- }
+ /**
+ * 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 newick property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNewick(String value) {
- this.newick = 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;
+ }
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * 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 fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * 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 fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * 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 fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
+ /**
+ * 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 threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBootstrap() {
- return showBootstrap;
- }
+ /**
+ * 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 showBootstrap property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="UserColourScheme"
+ * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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 showDistances property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDistances() {
- return showDistances;
- }
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return possible object is {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme()
+ {
+ return userColourScheme;
+ }
- /**
- * 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 userColourScheme property.
+ *
+ * @param value
+ * allowed object is {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value)
+ {
+ this.userColourScheme = value;
+ }
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked() {
- return markUnlinked;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * 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 id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isFitToWindow() {
- return fitToWindow;
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="AnnotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="autoUpdate"
+ * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="overview" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="residueColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="hiddenColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="conservationSelected"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charWidth"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="idWidthManuallyAdjusted"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="scaleProteinAsCdna"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="viewName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="gatheredViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="showComplementFeatures"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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;
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value) {
- this.fitToWindow = value;
- }
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
- /**
- * Gets the value of the currentTree property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCurrentTree() {
- return currentTree;
- }
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value) {
- this.currentTree = value;
- }
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
- /**
- * 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 = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
- /**
- * Sets the value of the columnWise property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColumnWise(Boolean value) {
- this.columnWise = value;
- }
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
- /**
- * Gets the value of the columnReference property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColumnReference() {
- return columnReference;
- }
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
- /**
- * Sets the value of the columnReference property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColumnReference(String value) {
- this.columnReference = value;
- }
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
- /**
- * 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 = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ @XmlAttribute(name = "charWidth")
+ protected Integer charWidth;
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ @XmlAttribute(name = "charHeight")
+ protected Integer charHeight;
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
- }
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "userColourScheme"
- })
- public static class UserColours {
+ @XmlAttribute(name = "idWidth")
+ protected Integer idWidth;
- @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
- protected JalviewUserColours userColourScheme;
- @XmlAttribute(name = "id")
- protected String id;
+ @XmlAttribute(name = "idWidthManuallyAdjusted")
+ protected Boolean idWidthManuallyAdjusted;
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return
- * possible object is
- * {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme() {
- return userColourScheme;
- }
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is
- * {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value) {
- this.userColourScheme = value;
- }
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
- }
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="overview" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @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 = "idWidth")
- protected Integer idWidth;
- @XmlAttribute(name = "idWidthManuallyAdjusted")
- protected Boolean idWidthManuallyAdjusted;
- @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;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
- /**
- * 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;
- }
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
- /**
- * 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;
- }
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
- /**
- * Gets the value of the overview property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.Viewport.Overview }
- *
- */
- public JalviewModel.Viewport.Overview getOverview() {
- return overview;
- }
+ @XmlAttribute(name = "width")
+ protected Integer width;
- /**
- * 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;
- }
+ @XmlAttribute(name = "height")
+ protected Integer height;
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isConservationSelected() {
- return conservationSelected;
- }
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value) {
- this.conservationSelected = value;
- }
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Gets the value of the pidSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPidSelected() {
- return pidSelected;
- }
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
- /**
- * 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 annotationColours property.
+ *
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBgColour() {
- return bgColour;
- }
+ /**
+ * 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;
+ }
- /**
- * 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 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 consThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ /**
+ * 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 consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ /**
+ * 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 pidThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected()
+ {
+ return conservationSelected;
+ }
- /**
- * 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 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;
+ }
- /**
- * 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;
+ }
+
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
- /**
- * 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 showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value)
+ {
+ this.showSequenceFeatures = 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 showNPfeatureTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip()
+ {
+ return showNPfeatureTooltip;
+ }
- /**
- * 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 showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value)
+ {
+ this.showNPfeatureTooltip = value;
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowAnnotation() {
- return showAnnotation;
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip()
+ {
+ return showDbRefTooltip;
+ }
- /**
- * 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 showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value)
+ {
+ this.showDbRefTooltip = 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 followHighlight property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight()
+ {
+ if (followHighlight == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followHighlight;
+ }
+ }
- /**
- * 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 followHighlight property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value)
+ {
+ this.followHighlight = 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 followSelection property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection()
+ {
+ if (followSelection == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followSelection;
+ }
+ }
- /**
- * 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 followSelection property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value)
+ {
+ this.followSelection = 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 showAnnotation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
- /**
- * 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 showAnnotation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value)
+ {
+ this.showAnnotation = 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 centreColumnLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels()
+ {
+ if (centreColumnLabels == null)
+ {
+ return false;
+ }
+ else
+ {
+ return centreColumnLabels;
+ }
+ }
- /**
- * 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 centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value)
+ {
+ this.centreColumnLabels = 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 showGroupConservation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation()
+ {
+ if (showGroupConservation == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConservation;
+ }
+ }
- /**
- * 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 showGroupConservation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value)
+ {
+ this.showGroupConservation = 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 showGroupConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus()
+ {
+ if (showGroupConsensus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConsensus;
+ }
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value)
+ {
+ this.showGroupConsensus = 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;
- }
- }
+ /**
+ * 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 ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = 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 startRes property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartRes() {
- return startRes;
- }
+ /**
+ * 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 startRes property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartRes(Integer value) {
- this.startRes = 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 startSeq property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartSeq() {
- return startSeq;
- }
+ /**
+ * 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 startSeq property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartSeq(Integer value) {
- this.startSeq = 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 charWidth property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getCharWidth() {
- return charWidth;
- }
+ /**
+ * 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 idWidth property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getIdWidth() {
- return idWidth;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Sets the value of the idWidth property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setIdWidth(Integer value) {
- this.idWidth = 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 idWidthManuallyAdjusted property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIdWidthManuallyAdjusted() {
- return idWidthManuallyAdjusted;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Sets the value of the idWidthManuallyAdjusted property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIdWidthManuallyAdjusted(Boolean value) {
- this.idWidthManuallyAdjusted = 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 scaleProteinAsCdna property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna() {
- if (scaleProteinAsCdna == null) {
- return true;
- } else {
- return scaleProteinAsCdna;
- }
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * 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 fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewName() {
- return viewName;
- }
+ /**
+ * Gets the value of the idWidth property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getIdWidth()
+ {
+ return idWidth;
+ }
- /**
- * 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 idWidth property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setIdWidth(Integer value)
+ {
+ this.idWidth = value;
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceSetId() {
- return sequenceSetId;
- }
+ /**
+ * Gets the value of the idWidthManuallyAdjusted property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIdWidthManuallyAdjusted()
+ {
+ return idWidthManuallyAdjusted;
+ }
- /**
- * 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 idWidthManuallyAdjusted property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIdWidthManuallyAdjusted(Boolean value)
+ {
+ this.idWidthManuallyAdjusted = 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam
- extends WebServiceParameterSet
- {
+ /**
+ * 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns {
-
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="autoUpdate" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam extends WebServiceParameterSet
+ {
+
+ @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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Overview {
-
- @XmlAttribute(name = "showHidden")
- protected Boolean showHidden;
- @XmlAttribute(name = "residueColour")
- protected Integer residueColour;
- @XmlAttribute(name = "gapColour")
- protected Integer gapColour;
- @XmlAttribute(name = "hiddenColour")
- protected Integer hiddenColour;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the showHidden property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowHidden() {
- return showHidden;
- }
-
- /**
- * Sets the value of the showHidden property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowHidden(Boolean value) {
- this.showHidden = value;
- }
-
- /**
- * Gets the value of the residueColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getResidueColour() {
- return residueColour;
- }
-
- /**
- * Sets the value of the residueColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setResidueColour(Integer value) {
- this.residueColour = value;
- }
-
- /**
- * Gets the value of the gapColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGapColour() {
- return gapColour;
- }
-
- /**
- * Sets the value of the gapColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGapColour(Integer value) {
- this.gapColour = value;
- }
-
- /**
- * Gets the value of the hiddenColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHiddenColour() {
- return hiddenColour;
- }
-
- /**
- * Sets the value of the hiddenColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHiddenColour(Integer value) {
- this.hiddenColour = value;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns
+ {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="residueColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="hiddenColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview
+ {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden()
+ {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value)
+ {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getResidueColour()
+ {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value)
+ {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGapColour()
+ {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value)
+ {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHiddenColour()
+ {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value)
+ {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
}
+ }
+
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="JalviewUserColours"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="JalviewUserColours"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="Version"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour"
+ * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType"
+ * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
+ * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="featureType" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="schemeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
- "version",
- "colour",
- "filter"
-})
-public class JalviewUserColours {
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
- @XmlElement(namespace = "")
- protected List<JalviewUserColours.Colour> colour;
+@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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour"
+ * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType"
+ * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
+ * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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 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 version property.
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getVersion() {
- return version;
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
+ }
+ else
+ {
+ return noValueColour;
+ }
}
/**
- * Sets the value of the version property.
+ * Sets the value of the noValueColour property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link NoValueColour }
+ *
*/
- public void setVersion(String value) {
- this.version = value;
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
}
/**
- * Gets the value of the colour property.
+ * Gets the value of the threshType property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make 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 ThresholdType }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getColour().add(newItem);
- * </pre>
+ */
+ public ThresholdType getThreshType()
+ {
+ return threshType;
+ }
+
+ /**
+ * Sets the value of the threshType property.
*
+ * @param value
+ * allowed object is {@link ThresholdType }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Colour }
+ */
+ public void setThreshType(ThresholdType value)
+ {
+ this.threshType = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
*
+ * @return possible object is {@link Float }
*
*/
- public List<JalviewUserColours.Colour> getColour() {
- if (colour == null) {
- colour = new ArrayList<JalviewUserColours.Colour>();
- }
- return this.colour;
+ public Float getThreshold()
+ {
+ return threshold;
}
/**
- * Gets the value of the filter property.
+ * Sets the value of the threshold property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make 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 Float }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getFilter().add(newItem);
- * </pre>
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the max property.
*
+ * @return possible object is {@link Float }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Filter }
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
*
+ * @param value
+ * allowed object is {@link Float }
*
*/
- public List<JalviewUserColours.Filter> getFilter() {
- if (filter == null) {
- filter = new ArrayList<JalviewUserColours.Filter>();
- }
- return this.filter;
+ public void setMax(Float value)
+ {
+ this.max = value;
}
/**
- * Gets the value of the schemeName property.
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getSchemeName() {
- return schemeName;
+ public Float getMin()
+ {
+ return min;
}
/**
- * Sets the value of the schemeName property.
+ * Sets the value of the min property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * 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 void setSchemeName(String value) {
- this.schemeName = value;
+ 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;
+ }
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * Gets the value of the autoScale property.
*
+ * @return possible object is {@link Boolean }
*
*/
- @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 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="featureType"
+ * use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the matcherSet property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link FeatureMatcherSet }
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
*
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
*
*/
- @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 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;
+ }
+
+ }
+
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="mapListType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="mapListType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="mapListFrom"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="mapFromUnit" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;attribute name="mapToUnit" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = {
- "mapListFrom",
- "mapListTo"
-})
-@XmlSeeAlso({
- Mapping.class
-})
-public class MapListType {
+@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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * 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: 2023.11.01 at 07:03:09 PM GMT
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Defines a mapping from the local frame to a matrix
- * and its associated data specified by MatrixType
- *
+ * Defines a mapping from the local frame to a matrix and its associated data
+ * specified by MatrixType
+ *
*
* <p>Java class for MapOnAMatrixType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="MapOnAMatrixType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="matrix" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="MapOnAMatrixType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="property"
+ * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="mapping"
+ * type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="matrix" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MapOnAMatrixType", propOrder = {
- "property",
- "mapping"
-})
-public class MapOnAMatrixType {
+@XmlType(name = "MapOnAMatrixType", propOrder = { "property", "mapping" })
+public class MapOnAMatrixType
+{
- protected List<Property> property;
- protected MapListType mapping;
- @XmlAttribute(name = "matrix", required = true)
- protected String matrix;
- @XmlAttribute(name = "id")
- protected String id;
+ protected List<Property> property;
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Property }
- *
- *
- */
- public List<Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Property>();
- }
- return this.property;
- }
+ protected MapListType mapping;
- /**
- * Gets the value of the mapping property.
- *
- * @return
- * possible object is
- * {@link MapListType }
- *
- */
- public MapListType getMapping() {
- return mapping;
- }
+ @XmlAttribute(name = "matrix", required = true)
+ protected String matrix;
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link MapListType }
- *
- */
- public void setMapping(MapListType value) {
- this.mapping = value;
- }
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * Gets the value of the matrix property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMatrix() {
- return matrix;
+ /**
+ * 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;
+ }
- /**
- * Sets the value of the matrix property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMatrix(String value) {
- this.matrix = value;
- }
+ /**
+ * Gets the value of the mapping property.
+ *
+ * @return possible object is {@link MapListType }
+ *
+ */
+ public MapListType getMapping()
+ {
+ return mapping;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is {@link MapListType }
+ *
+ */
+ public void setMapping(MapListType value)
+ {
+ this.mapping = 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 matrix property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMatrix()
+ {
+ return matrix;
+ }
+
+ /**
+ * Sets the value of the matrix property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMatrix(String value)
+ {
+ this.matrix = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
- * &lt;sequence&gt;
- * &lt;choice minOccurs="0"&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt;
- * &lt;element name="dseqFor"&gt;
- * &lt;simpleType&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * &lt;/element&gt;
- * &lt;/choice&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
+ * &lt;sequence&gt; &lt;choice minOccurs="0"&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt; &lt;element
+ * name="dseqFor"&gt; &lt;simpleType&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;/restriction&gt; &lt;/simpleType&gt;
+ * &lt;/element&gt; &lt;/choice&gt; &lt;/sequence&gt;
+ * &lt;attribute name="mappingType"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "sequence",
- "dseqFor"
-})
+@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
@XmlRootElement(name = "Mapping")
-public class Mapping
- extends MapListType
+public class Mapping extends MapListType
{
- @XmlElement(name = "Sequence")
- protected Sequence sequence;
- protected String dseqFor;
- @XmlAttribute(name = "mappingType")
- protected String mappingType;
+ @XmlElement(name = "Sequence")
+ protected Sequence sequence;
+
+ protected String dseqFor;
+
+ @XmlAttribute(name = "mappingType")
+ protected String mappingType;
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link Sequence }
- *
- */
- public Sequence getSequence() {
- return sequence;
- }
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link Sequence }
+ *
+ */
+ public Sequence getSequence()
+ {
+ return sequence;
+ }
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link Sequence }
- *
- */
- public void setSequence(Sequence value) {
- this.sequence = value;
- }
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link Sequence }
+ *
+ */
+ public void setSequence(Sequence value)
+ {
+ this.sequence = value;
+ }
- /**
- * Gets the value of the dseqFor property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDseqFor() {
- return dseqFor;
- }
+ /**
+ * Gets the value of the dseqFor property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDseqFor()
+ {
+ return dseqFor;
+ }
- /**
- * Sets the value of the dseqFor property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDseqFor(String value) {
- this.dseqFor = value;
- }
+ /**
+ * Sets the value of the dseqFor property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDseqFor(String value)
+ {
+ this.dseqFor = value;
+ }
- /**
- * Gets the value of the mappingType property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMappingType() {
- return mappingType;
- }
+ /**
+ * Gets the value of the mappingType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMappingType()
+ {
+ return mappingType;
+ }
- /**
- * Sets the value of the mappingType property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMappingType(String value) {
- this.mappingType = value;
- }
+ /**
+ * Sets the value of the mappingType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMappingType(String value)
+ {
+ this.mappingType = value;
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Represents matrix data imported to Jalview, and the
- * results of any derived calculations (independent of a particular
- * view
- * on the matrix).
- *
+ * Represents matrix data imported to Jalview, and the results of any derived
+ * calculations (independent of a particular view on the matrix).
+ *
*
* <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>
- * &lt;complexType name="MatrixType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="elements" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="treeMethod" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="MatrixType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="elements"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="groups" type="{http://www.w3.org/2001/XMLSchema}string"
+ * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="newick"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="property"
+ * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="rows" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; &lt;attribute
+ * name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer"
+ * /&gt; &lt;attribute name="treeMethod"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
+ * &lt;attribute name="id" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MatrixType", propOrder = {
- "elements",
- "groups",
- "newick",
- "property"
-})
-public class MatrixType {
+@XmlType(
+ name = "MatrixType",
+ propOrder =
+ { "elements", "groups", "newick", "property" })
+public class MatrixType
+{
- @XmlElement(required = true)
- protected String elements;
- protected List<String> groups;
- protected List<String> newick;
- protected List<Property> property;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "rows", required = true)
- protected BigInteger rows;
- @XmlAttribute(name = "cols", required = true)
- protected BigInteger cols;
- @XmlAttribute(name = "treeMethod")
- protected String treeMethod;
- @XmlAttribute(name = "cutHeight")
- protected Double cutHeight;
- @XmlAttribute(name = "id", required = true)
- protected String id;
+ @XmlElement(required = true)
+ protected String elements;
- /**
- * Gets the value of the elements property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getElements() {
- return elements;
- }
+ protected List<String> groups;
- /**
- * Sets the value of the elements property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setElements(String value) {
- this.elements = value;
- }
+ protected List<String> newick;
- /**
- * 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<Property> property;
- /**
- * 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;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * 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;
- }
+ @XmlAttribute(name = "rows", required = true)
+ protected BigInteger rows;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "cols", required = true)
+ protected BigInteger cols;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ @XmlAttribute(name = "treeMethod")
+ protected String treeMethod;
- /**
- * Gets the value of the rows property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getRows() {
- return rows;
- }
+ @XmlAttribute(name = "cutHeight")
+ protected Double cutHeight;
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setRows(BigInteger value) {
- this.rows = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the cols property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getCols() {
- return cols;
- }
+ /**
+ * Gets the value of the elements property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getElements()
+ {
+ return elements;
+ }
- /**
- * Sets the value of the cols property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setCols(BigInteger value) {
- this.cols = value;
- }
+ /**
+ * Sets the value of the elements property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setElements(String value)
+ {
+ this.elements = value;
+ }
- /**
- * Gets the value of the treeMethod property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTreeMethod() {
- return treeMethod;
+ /**
+ * 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;
+ }
- /**
- * 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 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;
+ }
- /**
- * Gets the value of the cutHeight property.
- *
- * @return
- * possible object is
- * {@link Double }
- *
- */
- public Double getCutHeight() {
- return cutHeight;
+ /**
+ * 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;
+ }
- /**
- * 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 type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * 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 id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>The following schema fragment specifies the expected content contained within this class.
- * <pre>
- * &lt;simpleType name="NoValueColour"&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;enumeration value="None"/&gt;
- * &lt;enumeration value="Min"/&gt;
- * &lt;enumeration value="Max"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * </pre>
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class. <pre> &lt;simpleType
+ * name="NoValueColour"&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
+ * value="None"/&gt; &lt;enumeration value="Min"/&gt;
+ * &lt;enumeration value="Max"/&gt; &lt;/restriction&gt;
+ * &lt;/simpleType&gt; </pre>
*
*/
@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum NoValueColour {
-
- @XmlEnumValue("None")
- NONE("None"),
- @XmlEnumValue("Min")
- MIN("Min"),
- @XmlEnumValue("Max")
- MAX("Max");
- private final String value;
-
- NoValueColour(String v) {
- value = v;
- }
-
- public 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 enum NoValueColour
+{
+
+ @XmlEnumValue("None")
+ NONE("None"), @XmlEnumValue("Min")
+ MIN("Min"), @XmlEnumValue("Max")
+ MAX("Max");
+
+ private final String value;
+
+ NoValueColour(String v)
+ {
+ value = v;
+ }
+
+ public String value()
+ {
+ return value;
+ }
+
+ public static NoValueColour fromValue(String v)
+ {
+ for (NoValueColour c : NoValueColour.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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 _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
- private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
- private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link MapListType }
- *
- */
- public MapListType createMapListType() {
- return new MapListType();
- }
-
- /**
- * Create an instance of {@link Sequence }
- *
- */
- public Sequence createSequence() {
- return new Sequence();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame }
- *
- */
- public AlcodonFrame createAlcodonFrame() {
- return new AlcodonFrame();
- }
-
- /**
- * Create an instance of {@link Annotation }
- *
- */
- public Annotation createAnnotation() {
- return new Annotation();
- }
-
- /**
- * Create an instance of {@link SequenceSet }
- *
- */
- public SequenceSet createSequenceSet() {
- return new SequenceSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet createFeatureMatcherSet() {
- return new FeatureMatcherSet();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours }
- *
- */
- public JalviewUserColours createJalviewUserColours() {
- return new JalviewUserColours();
- }
-
- /**
- * Create an instance of {@link Pdbentry }
- *
- */
- public Pdbentry createPdbentry() {
- return new Pdbentry();
- }
-
- /**
- * Create an instance of {@link Feature }
- *
- */
- public Feature createFeature() {
- return new Feature();
- }
-
- /**
- * Create an instance of {@link JalviewModel }
- *
- */
- public JalviewModel createJalviewModel() {
- return new JalviewModel();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings }
- *
- */
- public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
- return new JalviewModel.FeatureSettings();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer }
- *
- */
- public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
- return new JalviewModel.PcaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport }
- *
- */
- public JalviewModel.Viewport createJalviewModelViewport() {
- return new JalviewModel.Viewport();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq }
- *
- */
- public JalviewModel.JSeq createJalviewModelJSeq() {
- return new JalviewModel.JSeq();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
- *
- */
- public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
- return new JalviewModel.JSeq.RnaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids }
- *
- */
- public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
- return new JalviewModel.JSeq.Pdbids();
- }
-
- /**
- * Create an instance of {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme createAnnotationColourScheme() {
- return new AnnotationColourScheme();
- }
-
- /**
- * Create an instance of {@link PcaDataType }
- *
- */
- public PcaDataType createPcaDataType() {
- return new PcaDataType();
- }
-
- /**
- * Create an instance of {@link DoubleVector }
- *
- */
- public DoubleVector createDoubleVector() {
- return new DoubleVector();
- }
-
- /**
- * Create an instance of {@link DoubleMatrix }
- *
- */
- public DoubleMatrix createDoubleMatrix() {
- return new DoubleMatrix();
- }
-
- /**
- * Create an instance of {@link Mapping }
- *
- */
- public Mapping createMapping() {
- return new Mapping();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListFrom }
- *
- */
- public MapListType.MapListFrom createMapListTypeMapListFrom() {
- return new MapListType.MapListFrom();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListTo }
- *
- */
- public MapListType.MapListTo createMapListTypeMapListTo() {
- return new MapListType.MapListTo();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType() {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Sequence.DBRef }
- *
- */
- public Sequence.DBRef createSequenceDBRef() {
- return new Sequence.DBRef();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.Alcodon }
- *
- */
- public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
- return new AlcodonFrame.Alcodon();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.AlcodMap }
- *
- */
- public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
- return new AlcodonFrame.AlcodMap();
- }
-
- /**
- * Create an instance of {@link AnnotationElement }
- *
- */
- public AnnotationElement createAnnotationElement() {
- return new AnnotationElement();
- }
-
- /**
- * Create an instance of {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine createAnnotationThresholdLine() {
- return new Annotation.ThresholdLine();
- }
-
- /**
- * Create an instance of {@link MapOnAMatrixType }
- *
- */
- public MapOnAMatrixType createMapOnAMatrixType() {
- return new MapOnAMatrixType();
- }
-
- /**
- * Create an instance of {@link jalview.xml.binding.jalview.Property }
- *
- */
- public jalview.xml.binding.jalview.Property createProperty() {
- return new jalview.xml.binding.jalview.Property();
- }
-
- /**
- * Create an instance of {@link SequenceSet.SequenceSetProperties }
- *
- */
- public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
- return new SequenceSet.SequenceSetProperties();
- }
-
- /**
- * Create an instance of {@link MatrixType }
- *
- */
- public MatrixType createMatrixType() {
- return new MatrixType();
- }
-
- /**
- * Create an instance of {@link VAMSAS }
- *
- */
- public VAMSAS createVAMSAS() {
- return new VAMSAS();
- }
-
- /**
- * Create an instance of {@link FeatureMatcher }
- *
- */
- public FeatureMatcher createFeatureMatcher() {
- return new FeatureMatcher();
- }
-
- /**
- * Create an instance of {@link WebServiceParameterSet }
- *
- */
- public WebServiceParameterSet createWebServiceParameterSet() {
- return new WebServiceParameterSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
- return new FeatureMatcherSet.CompoundMatcher();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Colour }
- *
- */
- public JalviewUserColours.Colour createJalviewUserColoursColour() {
- return new JalviewUserColours.Colour();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Filter }
- *
- */
- public JalviewUserColours.Filter createJalviewUserColoursFilter() {
- return new JalviewUserColours.Filter();
- }
-
- /**
- * Create an instance of {@link Pdbentry.Property }
- *
- */
- public Pdbentry.Property createPdbentryProperty() {
- return new Pdbentry.Property();
- }
-
- /**
- * Create an instance of {@link Feature.OtherData }
- *
- */
- public Feature.OtherData createFeatureOtherData() {
- return new Feature.OtherData();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JGroup }
- *
- */
- public JalviewModel.JGroup createJalviewModelJGroup() {
- return new JalviewModel.JGroup();
- }
-
- /**
- * Create an instance of {@link JalviewModel.UserColours }
- *
- */
- public JalviewModel.UserColours createJalviewModelUserColours() {
- return new JalviewModel.UserColours();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Tree }
- *
- */
- public JalviewModel.Tree createJalviewModelTree() {
- return new JalviewModel.Tree();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
- *
- */
- public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
- return new JalviewModel.FeatureSettings.Setting();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Group }
- *
- */
- public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
- return new JalviewModel.FeatureSettings.Group();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
- *
- */
- public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
- return new JalviewModel.PcaViewer.SequencePoint();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.Axis }
- *
- */
- public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
- return new JalviewModel.PcaViewer.Axis();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
- return new JalviewModel.PcaViewer.SeqPointMin();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
- return new JalviewModel.PcaViewer.SeqPointMax();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
- *
- */
- public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
- return new JalviewModel.Viewport.HiddenColumns();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
- *
- */
- public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
- return new JalviewModel.Viewport.CalcIdParam();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.Overview }
- *
- */
- public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
- return new JalviewModel.Viewport.Overview();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- */
- public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
- return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- */
- public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
- return new JalviewModel.JSeq.Pdbids.StructureState();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
- public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
- return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
- public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
- return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
- public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
- return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
- }
+public class ObjectFactory
+{
+
+ private final static QName _JalviewModel_QNAME = new QName(
+ "www.jalview.org", "JalviewModel");
+
+ private final static QName _JalviewUserColours_QNAME = new QName(
+ "www.jalview.org/colours", "JalviewUserColours");
+
+ private final static QName _WebServiceParameterSet_QNAME = new QName(
+ "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.jalview
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link MapListType }
+ *
+ */
+ public MapListType createMapListType()
+ {
+ return new MapListType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence }
+ *
+ */
+ public Sequence createSequence()
+ {
+ return new Sequence();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame()
+ {
+ return new AlcodonFrame();
+ }
+
+ /**
+ * Create an instance of {@link Annotation }
+ *
+ */
+ public Annotation createAnnotation()
+ {
+ return new Annotation();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet }
+ *
+ */
+ public SequenceSet createSequenceSet()
+ {
+ return new SequenceSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet createFeatureMatcherSet()
+ {
+ return new FeatureMatcherSet();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours createJalviewUserColours()
+ {
+ return new JalviewUserColours();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry }
+ *
+ */
+ public Pdbentry createPdbentry()
+ {
+ return new Pdbentry();
+ }
+
+ /**
+ * Create an instance of {@link Feature }
+ *
+ */
+ public Feature createFeature()
+ {
+ return new Feature();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel }
+ *
+ */
+ public JalviewModel createJalviewModel()
+ {
+ return new JalviewModel();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
+ {
+ return new JalviewModel.FeatureSettings();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer }
+ *
+ */
+ public JalviewModel.PcaViewer createJalviewModelPcaViewer()
+ {
+ return new JalviewModel.PcaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport }
+ *
+ */
+ public JalviewModel.Viewport createJalviewModelViewport()
+ {
+ return new JalviewModel.Viewport();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq }
+ *
+ */
+ public JalviewModel.JSeq createJalviewModelJSeq()
+ {
+ return new JalviewModel.JSeq();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
+ {
+ return new JalviewModel.JSeq.RnaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
+ {
+ return new JalviewModel.JSeq.Pdbids();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme createAnnotationColourScheme()
+ {
+ return new AnnotationColourScheme();
+ }
+
+ /**
+ * Create an instance of {@link PcaDataType }
+ *
+ */
+ public PcaDataType createPcaDataType()
+ {
+ return new PcaDataType();
+ }
+
+ /**
+ * Create an instance of {@link DoubleVector }
+ *
+ */
+ public DoubleVector createDoubleVector()
+ {
+ return new DoubleVector();
+ }
+
+ /**
+ * Create an instance of {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix createDoubleMatrix()
+ {
+ return new DoubleMatrix();
+ }
+
+ /**
+ * Create an instance of {@link Mapping }
+ *
+ */
+ public Mapping createMapping()
+ {
+ return new Mapping();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListFrom }
+ *
+ */
+ public MapListType.MapListFrom createMapListTypeMapListFrom()
+ {
+ return new MapListType.MapListFrom();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListTo }
+ *
+ */
+ public MapListType.MapListTo createMapListTypeMapListTo()
+ {
+ return new MapListType.MapListTo();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType()
+ {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence.DBRef }
+ *
+ */
+ public Sequence.DBRef createSequenceDBRef()
+ {
+ return new Sequence.DBRef();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
+ {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
+ {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement()
+ {
+ return new AnnotationElement();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine createAnnotationThresholdLine()
+ {
+ return new Annotation.ThresholdLine();
+ }
+
+ /**
+ * Create an instance of {@link MapOnAMatrixType }
+ *
+ */
+ public MapOnAMatrixType createMapOnAMatrixType()
+ {
+ return new MapOnAMatrixType();
+ }
+
+ /**
+ * Create an instance of {@link jalview.xml.binding.jalview.Property }
+ *
+ */
+ public jalview.xml.binding.jalview.Property createProperty()
+ {
+ return new jalview.xml.binding.jalview.Property();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet.SequenceSetProperties }
+ *
+ */
+ public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
+ {
+ return new SequenceSet.SequenceSetProperties();
+ }
+
+ /**
+ * Create an instance of {@link MatrixType }
+ *
+ */
+ public MatrixType createMatrixType()
+ {
+ return new MatrixType();
+ }
+
+ /**
+ * Create an instance of {@link VAMSAS }
+ *
+ */
+ public VAMSAS createVAMSAS()
+ {
+ return new VAMSAS();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher createFeatureMatcher()
+ {
+ return new FeatureMatcher();
+ }
+
+ /**
+ * Create an instance of {@link WebServiceParameterSet }
+ *
+ */
+ public WebServiceParameterSet createWebServiceParameterSet()
+ {
+ return new WebServiceParameterSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
+ {
+ return new FeatureMatcherSet.CompoundMatcher();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Colour }
+ *
+ */
+ public JalviewUserColours.Colour createJalviewUserColoursColour()
+ {
+ return new JalviewUserColours.Colour();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Filter }
+ *
+ */
+ public JalviewUserColours.Filter createJalviewUserColoursFilter()
+ {
+ return new JalviewUserColours.Filter();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry.Property }
+ *
+ */
+ public Pdbentry.Property createPdbentryProperty()
+ {
+ return new Pdbentry.Property();
+ }
+
+ /**
+ * Create an instance of {@link Feature.OtherData }
+ *
+ */
+ public Feature.OtherData createFeatureOtherData()
+ {
+ return new Feature.OtherData();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JGroup }
+ *
+ */
+ public JalviewModel.JGroup createJalviewModelJGroup()
+ {
+ return new JalviewModel.JGroup();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.UserColours }
+ *
+ */
+ public JalviewModel.UserColours createJalviewModelUserColours()
+ {
+ return new JalviewModel.UserColours();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Tree }
+ *
+ */
+ public JalviewModel.Tree createJalviewModelTree()
+ {
+ return new JalviewModel.Tree();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+ *
+ */
+ public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
+ {
+ return new JalviewModel.FeatureSettings.Setting();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+ *
+ */
+ public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
+ {
+ return new JalviewModel.FeatureSettings.Group();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ */
+ public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
+ {
+ return new JalviewModel.PcaViewer.SequencePoint();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+ *
+ */
+ public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
+ {
+ return new JalviewModel.PcaViewer.Axis();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
+ {
+ return new JalviewModel.PcaViewer.SeqPointMin();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
+ {
+ return new JalviewModel.PcaViewer.SeqPointMax();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ */
+ public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
+ {
+ return new JalviewModel.Viewport.HiddenColumns();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ */
+ public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
+ {
+ return new JalviewModel.Viewport.CalcIdParam();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview createJalviewModelViewportOverview()
+ {
+ return new JalviewModel.Viewport.Overview();
+ }
+
+ /**
+ * Create an instance of
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
+ {
+ return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
+ {
+ return new JalviewModel.JSeq.Pdbids.StructureState();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
+ * }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link JalviewModel }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+ public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
+ {
+ return new JAXBElement<JalviewModel>(_JalviewModel_QNAME,
+ JalviewModel.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement
+ * }{@code <}{@link JalviewUserColours }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link JalviewUserColours }{@code >}
+ */
+ @XmlElementDecl(
+ namespace = "www.jalview.org/colours",
+ name = "JalviewUserColours")
+ public JAXBElement<JalviewUserColours> createJalviewUserColours(
+ JalviewUserColours value)
+ {
+ return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME,
+ JalviewUserColours.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement
+ * }{@code <}{@link WebServiceParameterSet }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link WebServiceParameterSet }{@code >}
+ */
+ @XmlElementDecl(
+ namespace = "www.jalview.org/xml/wsparamset",
+ name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
+ WebServiceParameterSet value)
+ {
+ return new JAXBElement<WebServiceParameterSet>(
+ _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
+ null, value);
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="PcaDataType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="PcaDataType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="pairwiseMatrix"
+ * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;element
+ * name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="eigenMatrix"
+ * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;/sequence&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
- "pairwiseMatrix",
- "tridiagonalMatrix",
- "eigenMatrix"
-})
-public class PcaDataType {
+@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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="pdbentry"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="pdbentry"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;element name="property"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="value" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="id" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
- "property"
-})
-@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
-})
-public class Pdbentry {
-
- protected List<Pdbentry.Property> property;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "file")
- protected String file;
-
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Pdbentry.Property }
- *
- *
- */
- public List<Pdbentry.Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Pdbentry.Property>();
- }
- return this.property;
+@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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="value" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
/**
- * Gets the value of the 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="property"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="property"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "property")
-public class Property {
+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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
+ * &lt;sequence&gt; &lt;element name="DBRef" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="source"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="canonical"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="dsseqid"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "dbRef"
-})
+@XmlType(name = "", propOrder = { "dbRef" })
@XmlRootElement(name = "Sequence")
-public class Sequence
- extends SequenceType
+public class Sequence extends SequenceType
{
- @XmlElement(name = "DBRef")
- protected List<Sequence.DBRef> dbRef;
- @XmlAttribute(name = "dsseqid")
- protected String dsseqid;
- @XmlAttribute(name = "biotype")
- protected String biotype;
+ @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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="source"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="canonical"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="sequenceSetProperties"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="Matrix"
+ * type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="datasetId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "sequence",
- "annotation",
- "sequenceSetProperties",
- "alcodonFrame",
- "matrix"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame",
+ "matrix" })
@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;
- @XmlElement(name = "Matrix")
- protected List<MatrixType> matrix;
- @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;
+
+ @XmlElement(name = "Matrix")
+ protected List<MatrixType> matrix;
+
+ @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 matrix property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the matrix property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getMatrix().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MatrixType }
- *
- *
- */
- public List<MatrixType> getMatrix() {
- if (matrix == null) {
- matrix = new ArrayList<MatrixType>();
- }
- return this.matrix;
+ /**
+ * Gets the value of the matrix property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the matrix property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getMatrix().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link MatrixType }
+ *
+ *
+ */
+ public List<MatrixType> getMatrix()
+ {
+ if (matrix == null)
+ {
+ matrix = new ArrayList<MatrixType>();
}
+ return this.matrix;
+ }
+
+ /**
+ * 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> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequenceSetProperties
+ {
+
+ @XmlAttribute(name = "key")
+ protected String key;
+
+ @XmlAttribute(name = "value")
+ protected String value;
/**
- * Gets the value of the 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>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * 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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="SequenceType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="SequenceType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="sequence"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = {
- "sequence",
- "name"
-})
-@XmlSeeAlso({
- Sequence.class
-})
-public class SequenceType {
-
- protected String sequence;
- protected String name;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "description")
- protected String description;
-
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequence() {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequence(String value) {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
+@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
+@XmlSeeAlso({ Sequence.class })
+public class SequenceType
+{
+
+ protected String sequence;
+
+ protected String name;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequence(String value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for ThresholdType.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <pre>
- * &lt;simpleType name="ThresholdType"&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;enumeration value="NONE"/&gt;
- * &lt;enumeration value="ABOVE"/&gt;
- * &lt;enumeration value="BELOW"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * </pre>
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class. <pre> &lt;simpleType
+ * name="ThresholdType"&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
+ * value="NONE"/&gt; &lt;enumeration value="ABOVE"/&gt;
+ * &lt;enumeration value="BELOW"/&gt; &lt;/restriction&gt;
+ * &lt;/simpleType&gt; </pre>
*
*/
@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum ThresholdType {
+public enum ThresholdType
+{
- NONE,
- ABOVE,
- BELOW;
+ NONE, ABOVE, BELOW;
- public String value() {
- return name();
- }
+ public String value()
+ {
+ return name();
+ }
- public static ThresholdType fromValue(String v) {
- return valueOf(v);
- }
+ public static ThresholdType fromValue(String v)
+ {
+ return valueOf(v);
+ }
}
// Generated on: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="VAMSAS"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="VAMSAS"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="Tree"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = {
- "tree",
- "sequenceSet"
-})
-public class VAMSAS {
+@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: 2023.11.01 at 07:03:09 PM GMT
//
-
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>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>
- * &lt;complexType name="WebServiceParameterSet"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/&gt;
- * &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="WebServiceParameterSet"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="Version"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="serviceURL"
+ * type="{http://www.w3.org/2001/XMLSchema}anyURI"
+ * maxOccurs="unbounded"/&gt; &lt;element name="parameters"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="name" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
- "version",
- "description",
- "serviceURL",
- "parameters"
-})
+@XmlType(
+ name = "WebServiceParameterSet",
+ namespace = "www.jalview.org/xml/wsparamset",
+ propOrder =
+ { "version", "description", "serviceURL", "parameters" })
@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
-})
-public class WebServiceParameterSet {
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
- @XmlElement(namespace = "")
- protected String description;
- @XmlElement(namespace = "", required = true)
- @XmlSchemaType(name = "anyURI")
- protected List<String> serviceURL;
- @XmlElement(namespace = "", required = true)
- protected String parameters;
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the serviceURL property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getServiceURL().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getServiceURL() {
- if (serviceURL == null) {
- serviceURL = new ArrayList<String>();
- }
- 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: 2023.11.01 at 07:03:09 PM GMT
//
-@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;
assertEquals(as.getAStr1(), as.getAStr2());
Mapping s1tos2 = as.getMappingFromS1(false);
- checkMapping(s1tos2,s1,s2);
+ checkMapping(s1tos2, s1, s2);
}
- public void checkMapping(Mapping s1tos2,SequenceI _s1,SequenceI _s2)
+ public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)
{
System.out.println(s1tos2.getMap().toString());
for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
{
- int p=s1tos2.getPosition(i);
- char s2c=_s2.getCharAt(i-_s2.getStart());
- char s1c=_s1.getCharAt(p-_s1.getStart());
- System.out.println("Position in s2: " + i +s2c
- + " maps to position in s1: " +p+s1c);
- assertEquals(s1c,s2c);
+ int p = s1tos2.getPosition(i);
+ char s2c = _s2.getCharAt(i - _s2.getStart());
+ char s1c = _s1.getCharAt(p - _s1.getStart());
+ System.out.println("Position in s2: " + i + s2c
+ + " maps to position in s1: " + p + s1c);
+ assertEquals(s1c, s2c);
}
}
+
@Test(groups = { "Functional" })
/**
* simple test that mapping from alignment corresponds identical positions.
assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
Mapping s1tos2 = as.getMappingFromS1(false);
- assertEquals("ASdFA",as.getAStr2());
+ assertEquals("ASdFA", as.getAStr2());
// verify mapping is consistent between original all-caps sequences
- checkMapping(s1tos2,s1,s2);
+ checkMapping(s1tos2, s1, s2);
}
@Test(groups = { "Functional" })
}
@AfterMethod(alwaysRun = true)
- public void tearDown()
+ public void tearDown()
{
try
{
}
*/
- @Test(groups = {"Functional","testTask3"}, dataProvider = "cmdLines")
+ @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines")
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
{
assertNull(ann.annotations[0]);
assertNull(ann.annotations[4]);
}
+
/**
* test the contact matrix nogroups property methods
*/
- @Test(groups= {"Functional"})
+ @Test(groups = { "Functional" })
public void test_contactMatrixGroups()
{
- AlignmentAnnotation aa = new AlignmentAnnotation("foo","foo desc",null);
+ AlignmentAnnotation aa = new AlignmentAnnotation("foo", "foo desc",
+ null);
assertTrue(aa.isShowGroupsForContactMatrix());
aa.setShowGroupsForContactMatrix(false);
assertFalse(aa.isShowGroupsForContactMatrix());
assertTrue(aa.isShowGroupsForContactMatrix());
// copy should not be updated
assertFalse(copy.isShowGroupsForContactMatrix());
-
-
+
}
}
verifyPAEmatrix(seq, aa, 0, 0, 4);
// test clustering
- paematrix.setGroupSet(GroupSet.makeGroups(paematrix, false,0.1f, false));
+ paematrix.setGroupSet(
+ GroupSet.makeGroups(paematrix, false, 0.1f, false));
// remap - test the MappableContactMatrix.liftOver method
SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
null);
// check for null on out of bounds
- ContactListI alcl = alForSeq.getContactListFor(newaa, newaa.annotations.length);
- assertNull(alcl,"Should've gotten null!");
+ ContactListI alcl = alForSeq.getContactListFor(newaa,
+ newaa.annotations.length);
+ assertNull(alcl, "Should've gotten null!");
// now check for mapping
alcl = alForSeq.getContactListFor(newaa, 1);
assertNotNull(alcl);
/**
* check mapping and resolution methods work
*/
- @Test(groups= {"Functional"})
- public void testMappableContactMatrix() {
+ @Test(groups = { "Functional" })
+ public void testMappableContactMatrix()
+ {
SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
- MapList map = new MapList(new int[]
- { 5, 9 }, new int[] { 1, 5 }, 1, 1);
- AlignmentAnnotation aa = newseq
- .addContactList(new PAEContactMatrix(newseq,map, PAEdata,null));
+ MapList map = new MapList(new int[] { 5, 9 }, new int[] { 1, 5 }, 1, 1);
+ AlignmentAnnotation aa = newseq.addContactList(
+ new PAEContactMatrix(newseq, map, PAEdata, null));
ContactListI clist = newseq.getContactListFor(aa, 4);
assertNotNull(clist);
clist = newseq.getContactListFor(aa, 3);
assertNull(clist);
-
+
ContactMatrixI cm = newseq.getContactMatrixFor(aa);
MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
int[] pos = mcm.getMappedPositionsFor(newseq, 0);
pos = mcm.getMappedPositionsFor(newseq, 1);
assertNotNull(pos);
- assertEquals(pos[0],4+newseq.getStart());
-
+ assertEquals(pos[0], 4 + newseq.getStart());
+
pos = mcm.getMappedPositionsFor(newseq, 6); // after end of matrix
assertNull(pos);
pos = mcm.getMappedPositionsFor(newseq, 5); // at end of matrix
assertNotNull(pos);
- assertEquals(pos[0],8+newseq.getStart());
+ assertEquals(pos[0], 8 + newseq.getStart());
SequenceI alseq = newseq.deriveSequence();
- alseq.insertCharAt(5,'-');
+ alseq.insertCharAt(5, '-');
pos = mcm.getMappedPositionsFor(alseq, 5); // at end of matrix
assertNotNull(pos);
- assertEquals(pos[0],8+newseq.getStart());
-
-
+ assertEquals(pos[0], 8 + newseq.getStart());
+
}
}
assertTrue(m.adjacent(seq1, 6, 8));
assertTrue(m.adjacent(seq1, 5, 8));
assertTrue(m.adjacent(seq1, 0, 1));
-
-
+
assertFalse(m.adjacent(seq2, 3, 3));
assertFalse(m.adjacent(null, 3, 3));
}
@Test(groups = { "Functional" })
public void testAppendResult()
{
- SequenceI seq1 = new Sequence("", "abcdefghijklm"),seq2=new Sequence("","defdefdefdef");
+ SequenceI seq1 = new Sequence("", "abcdefghijklm"),
+ seq2 = new Sequence("", "defdefdefdef");
SearchResultsI sr = new SearchResults();
sr.appendResult(seq1, 3, 5);
assertEquals(1, sr.getCount());
assertTrue(sr.appendResult(seq2, 7, 49));
assertTrue(sr.appendResult(seq2, 0, 30));
assertEquals(2, sr.getCount());
- int c=0;
- for (SearchResultMatchI sre: sr.getResults())
+ int c = 0;
+ for (SearchResultMatchI sre : sr.getResults())
{
c++;
}
- assertEquals(c,2);
-
+ assertEquals(c, 2);
+
}
+
/**
* Test for method that checks if search results matches a sequence region
*/
assertEquals("ABCDEF",
derived.getDatasetSequence().getSequenceAsString());
}
-
+
/**
* test that creating a copy of an existing sequence with dataset sequence and
* associated contact matrix yields annotation associated with the same
* contact matrix in the copy
*/
- @Test(groups= {"Functional"})
+ @Test(groups = { "Functional" })
public void testCopyPasteStyleDerivesequence_withcontactMatrixAnn()
{
- SequenceI seq1=new Sequence("seq1","ACDACDACD");
+ SequenceI seq1 = new Sequence("seq1", "ACDACDACD");
seq1.createDatasetSequence();
ContactMatrixI cm = new SeqDistanceContactMatrix(seq1.getLength());
- // addContactList needs to return annotation addable to the sequence reference it was called from
+ // addContactList needs to return annotation addable to the sequence
+ // reference it was called from
AlignmentAnnotation aann = seq1.addContactList(cm);
- assertTrue(aann.sequenceRef==seq1);
- assertEquals(1,seq1.getAnnotation().length);
+ assertTrue(aann.sequenceRef == seq1);
+ assertEquals(1, seq1.getAnnotation().length);
assertNotNull(seq1.getContactListFor(seq1.getAnnotation()[0], 1));
-
- SequenceI seq_derived=seq1.deriveSequence();
- assertEquals(1,seq_derived.getAnnotation().length);
- assertTrue(cm==seq_derived.getContactMatrixFor(seq_derived.getAnnotation()[0]));
- assertNotNull(seq_derived.getContactListFor(seq_derived.getAnnotation()[0], 1));
-
+
+ SequenceI seq_derived = seq1.deriveSequence();
+ assertEquals(1, seq_derived.getAnnotation().length);
+ assertTrue(cm == seq_derived
+ .getContactMatrixFor(seq_derived.getAnnotation()[0]));
+ assertNotNull(seq_derived
+ .getContactListFor(seq_derived.getAnnotation()[0], 1));
+
// copy paste actually uses the copy constructor .. so
-
- SequenceI seq_copied=new Sequence((Sequence)seq_derived);
- assertEquals(1,seq_copied.getAnnotation().length);
- assertTrue(cm==seq_copied.getContactMatrixFor(seq_copied.getAnnotation()[0]));
- assertNotNull(seq_copied.getContactListFor(seq_copied.getAnnotation()[0], 1));
-
-
+
+ SequenceI seq_copied = new Sequence((Sequence) seq_derived);
+ assertEquals(1, seq_copied.getAnnotation().length);
+ assertTrue(cm == seq_copied
+ .getContactMatrixFor(seq_copied.getAnnotation()[0]));
+ assertNotNull(
+ seq_copied.getContactListFor(seq_copied.getAnnotation()[0], 1));
+
}
@Test(groups = { "Functional" })
origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
toSeq.transferAnnotation(origSeq, null);
- assertEquals("DESCRIPTION",toSeq.getDescription());
+ assertEquals("DESCRIPTION", toSeq.getDescription());
toSeq = new Sequence("MYSEQ", "THISISASEQ");
toSeq.setDescription("unchanged");
toSeq.transferAnnotation(origSeq, null);
- assertEquals("unchanged",toSeq.getDescription());
-
+ assertEquals("unchanged", toSeq.getDescription());
+
assertTrue(toSeq.getDBRefs().size() == 1);
assertTrue(toSeq.getDBRefs().get(0).isCanonical());
+ " \"resolution\":2.2,\n"
+ " \"title\":\"Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal\"}]\n"
+ " }}" });
- mocks.add(new String[] {
- "https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4gs9+OR+6bvb+OR+8ck8+OR+8ck3+OR+6x3d+OR+8ck4+OR+6x28+OR+6i7r+OR+3h82+OR+6i7q+OR+6x21+OR+4xt2+OR+5kiz+OR+7q5v+OR+6x2h+OR+7q5x+OR+3f1n+OR+3f1o+OR+2a24+OR+3f1p+OR+1p97+OR+4ghi+OR+3h7w+OR+6d09+OR+6czw+OR+7ujv+OR+5tbm+OR+5ufp+OR+4pky+OR+6d0b+OR+6d0c+OR+6x37)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort="
- ,
- readJsonStringFromFile(
- "test/jalview/fts/threedbeacons/q99814_tdb_pdbfts_query_resp.txt")});
+ mocks.add(
+ new String[]
+ { "https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4gs9+OR+6bvb+OR+8ck8+OR+8ck3+OR+6x3d+OR+8ck4+OR+6x28+OR+6i7r+OR+3h82+OR+6i7q+OR+6x21+OR+4xt2+OR+5kiz+OR+7q5v+OR+6x2h+OR+7q5x+OR+3f1n+OR+3f1o+OR+2a24+OR+3f1p+OR+1p97+OR+4ghi+OR+3h7w+OR+6d09+OR+6czw+OR+7ujv+OR+5tbm+OR+5ufp+OR+4pky+OR+6d0b+OR+6d0c+OR+6x37)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=",
+ readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/q99814_tdb_pdbfts_query_resp.txt") });
} catch (Throwable e)
{
Assert.fail("Couldn't read mock data.", e);
System.out.println("Search summary : \n" + response.getSearchSummary());
// System.out.println(response.getSearchSummary().size());
}
-
+
}
assertEquals(0, ranges.getStartSeq());
assertEquals(2, ranges.getEndSeq());
}
- @Test(groups = {"Functional"})
+
+ @Test(groups = { "Functional" })
public void testGetSelectionAsNewSequences_withContactMatrices()
{
- SequenceI seq = new Sequence("seq","ACADA");
+ SequenceI seq = new Sequence("seq", "ACADA");
ContactMatrixI cmat = new SeqDistanceContactMatrix(5);
seq.addContactList(cmat);
- Alignment al = new Alignment(new SequenceI[] {seq.deriveSequence() });
+ Alignment al = new Alignment(new SequenceI[] { seq.deriveSequence() });
al.addAnnotation(al.getSequenceAt(0).getAnnotation()[0]);
- AlignFrame af = new AlignFrame(al,500,500);
-
+ AlignFrame af = new AlignFrame(al, 500, 500);
+
SequenceI selseqs[] = af.getViewport().getSelectionAsNewSequence();
assertNotNull(selseqs[0].getAnnotation());
assertNotNull(selseqs[0].getAnnotation()[0]);
- assertEquals(cmat,selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
-
- assertNotNull(selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
-
+ assertEquals(cmat,
+ selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
+
+ assertNotNull(
+ selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
+
// now select everything and test again
af.selectAllSequenceMenuItem_actionPerformed(null);
selseqs = af.getViewport().getSelectionAsNewSequence();
assertNotNull(selseqs[0].getAnnotation());
assertNotNull(selseqs[0].getAnnotation()[0]);
- assertEquals(cmat,selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
- assertNotNull(selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
+ assertEquals(cmat,
+ selseqs[0].getContactMatrixFor(selseqs[0].getAnnotation()[0]));
+ assertNotNull(
+ selseqs[0].getContactListFor(selseqs[0].getAnnotation()[0], 2));
}
}
/**
* Test the variant of calculateIdWidth that computes the longest of any
- * sequence name or annotation label width
- * FIXME: JAL-4291: test needs updating for JAL-244 and JAL-4091
+ * sequence name or annotation label width FIXME: JAL-4291: test needs
+ * updating for JAL-244 and JAL-4091
*/
- @Test(groups = "Functional",enabled=false)
+ @Test(groups = "Functional", enabled = false)
public void testCalculateIdWidth_withMaxWidth()
{
AlignViewportI av = af.alignPanel.getAlignViewport();
Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
}
+
@Test(groups = { "Functional", "Not-bamboo" })
public void testresetIdWidth()
{
assertEquals(w, af.alignPanel.getIdPanel().getWidth());
assertEquals(w, 115);
- // manually adjust
+ // manually adjust
af.viewport.setIdWidth(200);
w = af.alignPanel.calculateIdWidth().width;
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
assertEquals(w, af.alignPanel.getIdPanel().getWidth());
af.viewport.setIdWidth(-1);
af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
w = af.alignPanel.calculateIdWidth().width;
-
+
assertEquals(w, af.alignPanel.getIdPanel().getWidth());
- assertNotEquals(w,115);
+ assertNotEquals(w, 115);
}
+
@Test(groups = "Functional")
public void testSetOverviewTitle()
{
"<html>By Score (> 4.0)<br>" + simpleTooltip
+ "</br></html>");
}
- String fsfile="<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">",fsfile2="<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n<ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">";
- @Test(groups="Functional")
+
+ String fsfile = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">",
+ fsfile2 = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n<ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">";
+
+ @Test(groups = "Functional")
public void testIdentifyFeatureSettingsFile() throws Exception
{
- FileFormatI type = new IdentifyFile().identify(fsfile, DataSourceType.PASTE);
- assertTrue(FileFormat.FeatureSettings==type,"Feature settings file was identified as "+type);
+ FileFormatI type = new IdentifyFile().identify(fsfile,
+ DataSourceType.PASTE);
+ assertTrue(FileFormat.FeatureSettings == type,
+ "Feature settings file was identified as " + type);
type = new IdentifyFile().identify(fsfile2, DataSourceType.PASTE);
- assertTrue(FileFormat.FeatureSettings==type,"Feature settings file with newline was identified as "+type);
+ assertTrue(FileFormat.FeatureSettings == type,
+ "Feature settings file with newline was identified as " + type);
}
}
ScalePanel scalePanel = alignFrame.alignPanel.getScalePanel();
MouseEvent mouse = new MouseEvent(scalePanel, 0, 1, 0, 4, 0, 1, false);
-
+
// check the bounded lookup is not returning negatives
- assertEquals(alignFrame.alignPanel.getSeqPanel().findAlignmentColumn(mouse),0);
-
+ assertEquals(
+ alignFrame.alignPanel.getSeqPanel().findAlignmentColumn(mouse),
+ 0);
+
scalePanel.mousePressed(mouse);
scalePanel.mouseDragged(mouse);
assertEquals(testee.findColumn(evt), -1);
assertEquals(testee.findAlignmentColumn(evt), 0);
-
x = labelWidth;
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
0, false, 0);
assertEquals(testee.findColumn(evt), 0);
assertEquals(testee.findAlignmentColumn(evt), 0);
-
/*
* x over right edge of last residue (including scale left)
*/
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
0, false, 0);
assertEquals(testee.findColumn(evt), residuesWide - 1);
- assertEquals(testee.findAlignmentColumn(evt), residuesWide-1);
-
+ assertEquals(testee.findAlignmentColumn(evt), residuesWide - 1);
/*
* x over scale right (beyond drawn columns) results in -1
// on scale
assertEquals(testee.findColumn(evt), -1);
// return right-most column visible
- assertEquals(testee.findAlignmentColumn(evt), residuesWide2-1);
-
+ assertEquals(testee.findAlignmentColumn(evt), residuesWide2 - 1);
// todo add startRes offset, hidden columns
upSeq_fer1_maize
.addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
upSeq_fer1_maize.createDatasetSequence();
-
- upSeq_epas1_human = new Sequence("EPAS1_HUMAN","MTADKEKKRSSSERRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSS\n"
- + "VCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIR\n"
- + "ENLSLKNGSGFGKKSKDMSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVKVYNNCPPHNSLCGYKE\n"
- + "PLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSEN\n"
- + "MTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTE\n"
- + "SLFKPHLMAMNSIFDSSGKGAVSEKSNFLFTKLKEEPEELAQLAPTPGDAIISLDFGNQNFEESSAYGKAIL\n"
- + "PPSQPWATELRSHSTQSEAGSLPAFTVPQAAAPGSTTPSATSSSSSCSTPNSPEDYYTSLDNDLKIEVIEKL\n"
- + "FAMDTEAKDQCSTQTDFNELDLETLAPYIPMDGEDFQLSPICPEERLLAENPQSTPQHCFSAMTNIFQPLAP\n"
- + "VAPHSPFLLDKFQQQLESKKTEPEHRPMSSIFFDAGSKASLPPCCGQASTPLSSMGGRSNTQWPPDPPLHFG\n"
- + "PTKWAVGDQRTEFLGAAPLGPPVSPPHVSTFKTRSAKGFGARGPDVLSPAMVALSNKLKLKRQLEYEEQAFQ\n"
- + "DLSGGDPPGGSTSHLMWKRMKNLRGGSCPLMPDKPLSANVPNDKFTQNPMRGLGHPLRHLPLPQPPSAISPG\n"
- + "ENSKSRFPPQCYATQYQDYSLSSAHKVSGMASRLLGPSFESYLLPELTRYDCEVNVPVLGSSTLLQGGDLLR\n"
- + "ALDQAT");
- upSeq_epas1_human.setDescription("Endothelial PAS domain-containing protein 1");
+
+ upSeq_epas1_human = new Sequence("EPAS1_HUMAN",
+ "MTADKEKKRSSSERRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSS\n"
+ + "VCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIR\n"
+ + "ENLSLKNGSGFGKKSKDMSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVKVYNNCPPHNSLCGYKE\n"
+ + "PLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSEN\n"
+ + "MTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTE\n"
+ + "SLFKPHLMAMNSIFDSSGKGAVSEKSNFLFTKLKEEPEELAQLAPTPGDAIISLDFGNQNFEESSAYGKAIL\n"
+ + "PPSQPWATELRSHSTQSEAGSLPAFTVPQAAAPGSTTPSATSSSSSCSTPNSPEDYYTSLDNDLKIEVIEKL\n"
+ + "FAMDTEAKDQCSTQTDFNELDLETLAPYIPMDGEDFQLSPICPEERLLAENPQSTPQHCFSAMTNIFQPLAP\n"
+ + "VAPHSPFLLDKFQQQLESKKTEPEHRPMSSIFFDAGSKASLPPCCGQASTPLSSMGGRSNTQWPPDPPLHFG\n"
+ + "PTKWAVGDQRTEFLGAAPLGPPVSPPHVSTFKTRSAKGFGARGPDVLSPAMVALSNKLKLKRQLEYEEQAFQ\n"
+ + "DLSGGDPPGGSTSHLMWKRMKNLRGGSCPLMPDKPLSANVPNDKFTQNPMRGLGHPLRHLPLPQPPSAISPG\n"
+ + "ENSKSRFPPQCYATQYQDYSLSSAHKVSGMASRLLGPSFESYLLPELTRYDCEVNVPVLGSSTLLQGGDLLR\n"
+ + "ALDQAT");
+ upSeq_epas1_human
+ .setDescription("Endothelial PAS domain-containing protein 1");
upSeq_epas1_human
- .addDBRef(new DBRefEntry("UNIPROT", "0", "Q99814", null, true));
+ .addDBRef(new DBRefEntry("UNIPROT", "0", "Q99814", null, true));
upSeq_epas1_human.createDatasetSequence();
}
upSeq = null;
upSeq_r1ab = null;
upSeq_fer1_maize = null;
- upSeq_epas1_human=null;
+ upSeq_epas1_human = null;
}
@SuppressWarnings("deprecation")
pdbResponse);
assertEquals(upResponse.getNumberOfItemsFound(),
joinedResp.getNumberOfItemsFound());
-
+
// Special data test case
if (testUpSeq.getDisplayId(true)
.equals(upSeq_epas1_human.getDisplayId(true)))
{
setUp();
return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
- { upSeq_fer1_maize },{upSeq_epas1_human} };
+ { upSeq_fer1_maize },
+ { upSeq_epas1_human } };
}
@Test(groups = { "Functional" })
name = "abcde12[345a]fg";
AssertJUnit.assertEquals("abcde12345afg",
PDBStructureChooserQuerySource.sanitizeSeqName(name));
- }
+ }
}
}
- @Test(groups= {"Functional"})
+ @Test(groups = { "Functional" })
public void testRnamlSeqImport() throws IOException
{
- RnamlFile parser = new RnamlFile("examples/testdata/7WKP-rna1.xml", DataSourceType.FILE);
- SequenceI[] seqs = parser.getSeqsAsArray();
+ RnamlFile parser = new RnamlFile("examples/testdata/7WKP-rna1.xml",
+ DataSourceType.FILE);
+ SequenceI[] seqs = parser.getSeqsAsArray();
assertNotNull(seqs);
- assertEquals(seqs.length,1);
- assertEquals(seqs[0].getEnd()-seqs[0].getStart()+1,seqs[0].getSequence().length);
+ assertEquals(seqs.length, 1);
+ assertEquals(seqs[0].getEnd() - seqs[0].getStart() + 1,
+ seqs[0].getSequence().length);
}
}
assertTrue(report.startsWith("<i>\n" + "<br/>\n" + "UNIPROT P30410,\n"
+ " P30411,\n" + " P30412,\n" + " P30413,...<br/>\n"
+ "PDB0 3iu1<br/>\n" + "PDB1 3iu1<br/>"));
- assertTrue(report.endsWith("PDB3 3iu1<br/>\n"+"PDB4,...<br/>\n"
+ assertTrue(report.endsWith("PDB3 3iu1<br/>\n" + "PDB4,...<br/>\n"
+ "(Output Sequence Details to list all database references)\n"
+ "</i>"));
}
cacheBox.addItem(testInput);
cacheBox.setSelectedItem(testInput);
cacheBox.updateCache();
- boolean done[]=new boolean[] { false };
+ boolean done[] = new boolean[] { false };
// this event gets processed after updateCache's update event on the swing
// thread
SwingUtilities.invokeLater(() -> {
- done[0]=true;
+ done[0] = true;
});
- long t=0;
- while (!done[0] && t<200)
+ long t = 0;
+ while (!done[0] && t < 200)
{
- try {
+ try
+ {
Thread.sleep(7);
t++;
- } catch (InterruptedException e)
- {
- e.printStackTrace();
- }
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
}
if (!done[0])
{
Assert.fail("Giving up after 1.4s waiting for cache to be updated.");
}
-
+
LinkedHashSet<String> foundCache = appCache
.getAllCachedItemsFor(TEST_CACHE_KEY);
Assert.assertTrue(foundCache.contains(testInput));
@Test(groups = { "Functional" })
public void testMatrixToFloatsAndBack()
{
- int imax=2000;
- int i=imax;
- SequenceI sq = new Sequence("dummy","SEQ");
- while (sq.getLength()<i)
+ int imax = 2000;
+ int i = imax;
+ SequenceI sq = new Sequence("dummy", "SEQ");
+ while (sq.getLength() < i)
{
- sq.setSequence(sq.getSequenceAsString()+'Q');
+ sq.setSequence(sq.getSequenceAsString() + 'Q');
}
float[][] paevals = new float[i][i];
for (i = imax - 1; i >= 0; i--)
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
assertEquals(vals[4][3], paevals[4][3]);
-
+
// test recovery
- for (i=0;i<imax;i++)
+ for (i = 0; i < imax; i++)
{
- for (int j=0;j<imax;j++)
+ for (int j = 0; j < imax; j++)
{
- assertEquals(vals[i][j],paevals[i][j]);
+ assertEquals(vals[i][j], paevals[i][j]);
}
}
}
+
@Test(groups = { "Functional" })
public void testPAEsaveRestore() throws Exception
{
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
assertEquals(vals[4][3], paevals[4][3]);
- dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false, 0.5f, false));
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
// verify no duplicate PAE matrix data when new view created and saved
-
+
// add reference annotations to view first, then copy
- AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null);
-
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0),
+ newSeq.getAnnotation()[0], null);
+
AlignmentViewPanel newview = af.newView("copy of PAE", true);
-
+
// redundant asserts here check all is good with the new view firest...
AlignmentI newviewAl = newview.getAlignment();
SequenceI newviewSeq = newviewAl.getSequenceAt(0);
Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph);
// check we have just one contact matrix mapping
Assert.assertEquals(newviewSeq.getContactMaps().size(), 1);
-
+
// and can be found for the annotation on the sequence
ContactMatrixI newviewMat = newviewSeq
.getContactMatrixFor(newviewSeq.getAnnotation()[0]);
Assert.assertNotNull(newviewMat);
Assert.assertTrue(newviewMat == restoredMat);
-
- // save the two views and restore. Now look at visible annotation to check all views have shared refs.
-
+
+ // save the two views and restore. Now look at visible annotation to check
+ // all views have shared refs.
+
tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews",
".jvp");
new Jalview2XML(false).saveState(tfile);
AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0];
newviewAl = af.getAlignPanels().get(1).getAlignment();
- AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0];
+ AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0)
+ .getAnnotation()[0];
- // annotations are shared across alignment views - so should still have an identical pair of annotations.
- Assert.assertTrue(view1aa==view2aa);
+ // annotations are shared across alignment views - so should still have an
+ // identical pair of annotations.
+ Assert.assertTrue(view1aa == view2aa);
// identical annotations means identical contact matrix mappings
- Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
+ Assert.assertEquals(
+ newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
- // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held.
+ // TODO Verify when distinct mappable PAEs are created, only one PAE dataset
+ // is actually held.
// Assert.assertTrue(view1aa!=view2aa);
// restoredMat = newAl.getContactMatrixFor(view1aa);
// newviewMat = newviewAl.getContactMatrixFor(view2aa);
// Assert.assertTrue(restoredMat!=newviewMat);
-
+
}
@Test(groups = "Functional")
- public void testStoreAndRestoreIDwidthAndAnnotationHeight() throws IOException
+ public void testStoreAndRestoreIDwidthAndAnnotationHeight()
+ throws IOException
{
Desktop.instance.closeAll_actionPerformed(null);
final String SECONDVIEW = "With Diffferent IDwidth";
// create a new tempfile
File tempfile = File.createTempFile("jvIdWidthStoreRestore", "jvp");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile.jvp", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ // FIXME JAL-4281 test made platform dependent to pass, but probably
+ // shouldn't be platform dependent
+ assertEquals(af.alignPanel.getAlignViewport().getIdWidth(),
+ Platform.isAMacAndNotJS() ? 144 : 138,
+ "Legacy project import should have fixed ID width");
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("examples/exampleFile.jvp",
- DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- // FIXME JAL-4281 test made platform dependent to pass, but probably shouldn't be platform dependent
- assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), Platform.isAMacAndNotJS() ? 144 : 138,
- "Legacy project import should have fixed ID width");
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
-
-
- af.alignPanel.getAlignViewport().setIdWidth(100);
- af.alignPanel.updateLayout();
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
-
- Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
- tempfile.delete();
- jv2xml.saveState(tempfile);
- assertTrue(jv2xml.errorMessage == null,
- "Failed to save dummy project with PCA: test broken");
- af = null;
- // load again.
- Desktop.instance.closeAll_actionPerformed(null);
- af = new FileLoader().LoadFileWaitTillLoaded(
- tempfile.getCanonicalPath(), DataSourceType.FILE);
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas()
- .isManuallyAdjusted());
- assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 100,
- "New project exported and import should have adjusted ID width");
-
- af.alignPanel.getAlignViewport().setIdWidth(100);
- af.alignPanel.updateLayout();
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
-
- // now make it autoadjusted
- af.alignPanel.getAlignViewport().setIdWidth(-1);
- af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
- af.alignPanel.updateLayout();
- assertFalse(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
- assertTrue(af.alignPanel.getAlignViewport().getIdWidth()>-1,
- "New project exported and import should have adjusted ID width");
-
- jv2xml = new jalview.project.Jalview2XML(false);
- tempfile.delete();
- jv2xml.saveState(tempfile);
- assertTrue(jv2xml.errorMessage == null,
- "Failed to save dummy project with PCA: test broken");
- af = null;
- // load again.
- Desktop.instance.closeAll_actionPerformed(null);
- af = new FileLoader().LoadFileWaitTillLoaded(
- tempfile.getCanonicalPath(), DataSourceType.FILE);
- assertFalse(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
- assertTrue(af.alignPanel.getAlignViewport().getIdWidth()>-1,
- "New project exported and import should have adjusted ID width");
+ af.alignPanel.getAlignViewport().setIdWidth(100);
+ af.alignPanel.updateLayout();
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+ Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
+ tempfile.delete();
+ jv2xml.saveState(tempfile);
+ assertTrue(jv2xml.errorMessage == null,
+ "Failed to save dummy project with PCA: test broken");
+ af = null;
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 100,
+ "New project exported and import should have adjusted ID width");
+
+ af.alignPanel.getAlignViewport().setIdWidth(100);
+ af.alignPanel.updateLayout();
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+ // now make it autoadjusted
+ af.alignPanel.getAlignViewport().setIdWidth(-1);
+ af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
+ af.alignPanel.updateLayout();
+ assertFalse(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1,
+ "New project exported and import should have adjusted ID width");
+
+ jv2xml = new jalview.project.Jalview2XML(false);
+ tempfile.delete();
+ jv2xml.saveState(tempfile);
+ assertTrue(jv2xml.errorMessage == null,
+ "Failed to save dummy project with PCA: test broken");
+ af = null;
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ assertFalse(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1,
+ "New project exported and import should have adjusted ID width");
}
}
public class ContactGeometryTest
{
- @Test(groups="Functional")
+ @Test(groups = "Functional")
public void testCoverageofRange()
{
// a really dumb test to make sure we really cover the requested pixel and
}
}
}
+
@Test(groups = "Functional")
public void testContactGeometry()
{
SequenceI sq = new Sequence("a", "SSSQ");
MappableContactMatrixI cm = new SeqDistanceContactMatrix(4);
AlignmentAnnotation cm_aan = sq.addContactList(cm);
- checkConsistencyFor(sq,cm_aan);
+ checkConsistencyFor(sq, cm_aan);
// Also check all is good when there's a sequence mapping involved
- MappableContactMatrixI newcm=cm.liftOver(sq,
+ MappableContactMatrixI newcm = cm.liftOver(sq,
new Mapping(sq, new MapList(new int[]
{ 1, 4 }, new int[] { 1, 4 }, 1, 1)));
AlignmentAnnotation mapped_cm = sq.addContactList(newcm);
- checkConsistencyFor(sq,mapped_cm);
+ checkConsistencyFor(sq, mapped_cm);
}
+
// Do some asserts for a sequence and a contact matrix
private void checkConsistencyFor(SequenceI sq, AlignmentAnnotation cm_aan)
{
- int col=1;
+ int col = 1;
ContactListI cl = sq.getContactListFor(cm_aan, col);
assertNotNull(cl);
- assertEquals(cl.getContactHeight(),4);
-
- // Map contacts 0 to 3 to a tiny range and check
- ContactGeometry testee = new ContactGeometry(cl,2);
- assertEquals(testee.contacts_per_pixel,2d);
+ assertEquals(cl.getContactHeight(), 4);
+
+ // Map contacts 0 to 3 to a tiny range and check
+ ContactGeometry testee = new ContactGeometry(cl, 2);
+ assertEquals(testee.contacts_per_pixel, 2d);
ContactGeometry.contactInterval lastInterval = testee.mapFor(1);
- assertEquals(lastInterval.cStart,2);
- assertEquals(lastInterval.cEnd,3);
- assertEquals(lastInterval.pStart,1);
- assertEquals(lastInterval.pEnd,1);
- ContactGeometry.contactInterval another = testee.mapFor(1,2);
- assertEquals(lastInterval,another);
+ assertEquals(lastInterval.cStart, 2);
+ assertEquals(lastInterval.cEnd, 3);
+ assertEquals(lastInterval.pStart, 1);
+ assertEquals(lastInterval.pEnd, 1);
+ ContactGeometry.contactInterval another = testee.mapFor(1, 2);
+ assertEquals(lastInterval, another);
// Also check for a big pixel range
testee = new ContactGeometry(cl, 395);
lastInterval = testee.mapFor(390, 395); // 395 is one over limit.
assertNotNull(lastInterval);
- assertEquals(lastInterval.cEnd,3);
- assertEquals(lastInterval.pEnd,394);
+ assertEquals(lastInterval.cEnd, 3);
+ assertEquals(lastInterval.pEnd, 394);
// Map contacts 0 to 3 to Pixels 0-9, 10-19, 20-29, 30-39
testee = new ContactGeometry(cl, 40);
// verify mapping from pixel to contacts
-
+
// renderer thinks base 0 for pixel coordinates
// contact coordinates are base 1
for (int p = 0; p < 40; p++)
{
- int expectC=(p / 10);
- int expectP=(expectC)*10;
+ int expectC = (p / 10);
+ int expectP = (expectC) * 10;
ContactGeometry.contactInterval ci_at = testee.mapFor(p),
ci_from = testee.mapFor(p, p);
assertNotNull(ci_at);
// mapFor and map should locate the same pixel window
- assertEquals(ci_at.cStart, expectC,"Different cStart at position "+p);
- assertEquals(ci_at.cEnd, expectC,"Different cEnd at position "+p);
- assertEquals(ci_at.pStart,expectP, "Different pStart at position "+p);
- assertEquals(ci_at.pEnd,expectP+9, "Different pEnd at position "+p);
-
- assertEquals(ci_from,ci_at, "Different contactIntervals at position "+p);
+ assertEquals(ci_at.cStart, expectC,
+ "Different cStart at position " + p);
+ assertEquals(ci_at.cEnd, expectC, "Different cEnd at position " + p);
+ assertEquals(ci_at.pStart, expectP,
+ "Different pStart at position " + p);
+ assertEquals(ci_at.pEnd, expectP + 9,
+ "Different pEnd at position " + p);
+
+ assertEquals(ci_from, ci_at,
+ "Different contactIntervals at position " + p);
// also test getRangeFor
ContactRange cr = cl.getRangeFor(ci_at.cStart, ci_at.cEnd);
- assertEquals(cr.getFrom_column(),cr.getTo_column());
- assertEquals((double) cr.getMean(),(double)Math.abs(col-cr.getFrom_column()), "Didn't resolve expected value at position "+p);
+ assertEquals(cr.getFrom_column(), cr.getTo_column());
+ assertEquals((double) cr.getMean(),
+ (double) Math.abs(col - cr.getFrom_column()),
+ "Didn't resolve expected value at position " + p);
}
-
+
ContactGeometry.contactInterval ci_at0 = testee.mapFor(0);
ContactGeometry.contactInterval ci_at9 = testee.mapFor(9);
assertNotNull(ci_at9);
-
- assertEquals(ci_at0,ci_at9);
+
+ assertEquals(ci_at0, ci_at9);
// Adjacent cell
ContactGeometry.contactInterval ci_at10 = testee.mapFor(10);
ContactGeometry.contactInterval ci_at11 = testee.mapFor(11);
assertNotNull(ci_at11);
- assertEquals(ci_at11,ci_at10,"Off-by-one in ContactGeometry mapping.");
+ assertEquals(ci_at11, ci_at10,
+ "Off-by-one in ContactGeometry mapping.");
+
+ assertNotEquals(ci_at0, ci_at10,
+ "Expected adjacent cells to be not equal.");
- assertNotEquals(ci_at0,ci_at10,"Expected adjacent cells to be not equal.");
-
// verify adjacent window is mapped
- assertEquals(ci_at11.cStart,ci_at9.cStart+1);
-
- assertEquals(ci_at9.cEnd+1,ci_at11.cStart);
- assertEquals(ci_at9.cEnd+1,ci_at11.cEnd);
-
+ assertEquals(ci_at11.cStart, ci_at9.cStart + 1);
+
+ assertEquals(ci_at9.cEnd + 1, ci_at11.cStart);
+ assertEquals(ci_at9.cEnd + 1, ci_at11.cEnd);
+
// verify interval/intersection
// column selection is base 0
ColumnSelection cs = new ColumnSelection();
cs.removeElement(2);
assertFalse(testee.intersects(testee.mapFor(21), cs, null, mask));
mask = !mask;
- } while (!mask);
-
+ } while (!mask);
+
}
}
SiftsSettings.setCacheThresholdInDays("2");
SiftsSettings.setFailSafePIDThreshold("70");
PDBfile pdbFile;
-
+
pdbFile = new PDBfile(false, false, false,
"test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
- // TODO: this uses a network connection - we should mock the sifts testPDBId.xml.gz
+ // TODO: this uses a network connection - we should mock the sifts
+ // testPDBId.xml.gz
siftsClient = new SiftsClient(pdbFile);
}
{
siftsClient = null;
}
-
- @Test(groups= {"Functional"})
- public void testSIFTsDownloadURL() {
+
+ @Test(groups = { "Functional" })
+ public void testSIFTsDownloadURL()
+ {
String expectedUrl = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/xy/1xyz.sifts.xml.gz";
- Assert.assertEquals(SiftsClient.getDownloadUrlFor("1xyz.sifts.xml.gz"), expectedUrl);
+ Assert.assertEquals(SiftsClient.getDownloadUrlFor("1xyz.sifts.xml.gz"),
+ expectedUrl);
}
@Test(groups = { "Network" })
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
DBRefEntry invalidDBRef = new DBRefEntry();
- invalidDBRef.setAccessionId("BLAR"); // note no version is set, so also invalid
+ invalidDBRef.setAccessionId("BLAR"); // note no version is set, so also
+ // invalid
invalidTestSeq.addDBRef(invalidDBRef);
siftsClient.getValidSourceDBRef(invalidTestSeq);
}
git://source.jalview.org / jalview.git / commitdiff