<xs:element name="JGroup" minOccurs="0"
maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence>
- <xs:element name="seq" type="xs:string"
- maxOccurs="unbounded" />
+ <xs:sequence>
+ <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
+ <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
+ minOccurs="0" maxOccurs="1" />
</xs:sequence>
<xs:attribute name="start" type="xs:int" />
<xs:attribute name="end" type="xs:int" />
<xs:element name="Viewport" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
- <xs:element name="AnnotationColours"
- minOccurs="0">
- <xs:complexType>
- <xs:attribute name="aboveThreshold"
- type="xs:int" />
- <xs:attribute name="annotation"
- type="xs:string" />
- <xs:attribute name="minColour"
- type="xs:int" />
- <xs:attribute name="maxColour"
- type="xs:int" />
- <xs:attribute name="colourScheme"
- type="xs:string" />
- <xs:attribute name="threshold"
- type="xs:float" />
- <xs:attribute name="perSequence"
- type="xs:boolean"
- use="optional" />
- <xs:attribute name="predefinedColours"
- type="xs:boolean"
- use="optional" />
- </xs:complexType>
+ <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
+ minOccurs="0" maxOccurs="1">
</xs:element>
<xs:element name="hiddenColumns"
minOccurs="0" maxOccurs="unbounded">
<xs:attribute name="xpos" type="xs:int"/>
<xs:attribute name="ypos" type="xs:int"/>
</xs:attributeGroup>
+ <xs:complexType name="AnnotationColourScheme">
+ <xs:attribute name="aboveThreshold" type="xs:int" />
+ <xs:attribute name="annotation" type="xs:string" />
+ <xs:attribute name="minColour" type="xs:int" />
+ <xs:attribute name="maxColour" type="xs:int" />
+ <xs:attribute name="colourScheme" type="xs:string" />
+ <xs:attribute name="threshold" type="xs:float" />
+ <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
+ <xs:attribute name="predefinedColours" type="xs:boolean"
+ use="optional" />
+ </xs:complexType>
+
</xs:schema>
residueHash.put(PID_GAPS, new Float(percentage));
if (nongap>0) {
+ // calculate for non-gapped too
percentage = ((float) maxCount * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
}
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
result[i] = residueHash;
}
}
import java.util.Hashtable;
import java.util.Map;
+import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
void setColumnSelection(ColumnSelection cs);
+ void setConservation(Conservation cons);
+
}
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
-
+ applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+
seqLimits.setState(viewport.showJVSuffix);
if (applet != null)
{
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
+ viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background"));
+ }
if (viewport.getConservationSelected())
{
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs.setConservationApplied(true);
+ viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
-
}
else
{
- cs.setConservation(null);
+ cs.setConservationApplied(false);
}
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
-
}
viewport.setGlobalColourScheme(cs);
}
}
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- public int getThreshold()
- {
- return threshold;
- }
-
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- public int getIncrement()
- {
- return increment;
- }
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
package jalview.appletgui;
import java.util.*;
-
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println("blob done "+ (System.currentTimeMillis()-start));
}
float value = slider.getValue();
+ List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.removeElement(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.addElement(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
}
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
}
return;
}
- ColourSchemeI toChange = null;
+ ColourSchemeI toChange = cs;
Iterator<SequenceGroup> allGroups = null;
if (allGroupsCheck.getState())
{
allGroups = ap.av.getAlignment().getGroups().listIterator();
}
- else
- {
- toChange = cs;
- }
- do
+ while (toChange != null)
{
- if (allGroups != null)
- {
- toChange = allGroups.next().cs;
- }
-
if (forConservation)
{
toChange.setConservationInc(i);
{
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
-
- } while (allGroups != null && allGroups.hasNext());
+ if (allGroups != null && allGroups.hasNext())
+ {
+ while ((toChange = allGroups.next().cs) == null
+ && allGroups.hasNext())
+ ;
+ }
+ else
+ {
+ toChange = null;
+ }
+ }
ap.seqPanel.seqCanvas.repaint();
slider.setFont(new java.awt.Font("Verdana", 0, 11));
slider.setOrientation(0);
valueField.setFont(new java.awt.Font("Verdana", 0, 11));
- valueField.setText(" ");
- valueField.addActionListener(this);
+ valueField.setText(" ");
+ valueField.addActionListener(this);
+ valueField.setColumns(3);
label.setFont(new java.awt.Font("Verdana", 0, 11));
label.setText(MessageManager.getString("label.set_this_label_text"));
jPanel1.setLayout(borderLayout1);
return;
}
}
-
+ sg.setContext(this);
groups.add(sg);
}
}
{
removeAnnotationForGroup(null);
}
+ for (SequenceGroup sg:groups) {
+ sg.setContext(null);
+ }
groups.clear();
}
}
{
removeAnnotationForGroup(g);
groups.remove(g);
+ g.setContext(null);
}
}
}
{
return 0;
}
+
+/* In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+@Override
+public AnnotatedCollectionI getContext()
+{
+ return dataset;
+}
}
Iterable<AlignmentAnnotation> findAnnotation(String calcId);
+ /**
+ * context for this annotated collection
+ * @return null or the collection upon which this collection is defined (e.g. alignment, parent group).
+ */
+ AnnotatedCollectionI getContext();
}
}
/**
- * Max Gaps Threshold for performing a conservation calculation TODO: make
- * this a configurable property - or global to an alignment view
+ * Max Gaps Threshold (percent) for performing a conservation calculation
*/
private int consPercGaps = 25;
/**
+ * @return Max Gaps Threshold for performing a conservation calculation
+ */
+ public int getConsPercGaps()
+ {
+ return consPercGaps;
+ }
+
+ /**
+ * set Max Gaps Threshold (percent) for performing a conservation calculation
+ * @param consPercGaps
+ */
+ public void setConsPercGaps(int consPercGaps)
+ {
+ this.consPercGaps = consPercGaps;
+ }
+
+ /**
* calculate residue conservation for group - but only if necessary.
*/
public void recalcConservation()
{
return;
}
- if (cs != null)
- {
- cs.alignmentChanged(this, null);
- }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
if (cs != null)
{
cs.setConsensus(cnsns);
- cs.alignmentChanged(this, null);
}
if ((conservation != null)
if (cs.conservationApplied())
{
cs.setConservation(c);
- cs.alignmentChanged(this, null);
}
}
}
+ if (cs != null)
+ {
+ cs.alignmentChanged(context!=null ? context : this, null);
+ }
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
for (SequenceI seq : (Vector<SequenceI>) sequences)
{
- for (AlignmentAnnotation al : seq.getAnnotation())
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
{
- if (al.groupRef == this)
+ for (AlignmentAnnotation al : aa)
{
- annot.add(al);
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
}
}
}
{
sequences.clear();
}
+ private AnnotatedCollectionI context;
+ /**
+ * set the alignment or group context for this group
+ * @param context
+ */
+ public void setContext(AnnotatedCollectionI context)
+ {
+ this.context = context;
+ }
+ /* (non-Javadoc)
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return context;
+ }
}
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
-
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
}
else
{
return;
}
- Hashtable<String,AlignFrame> dsses = new Hashtable<String,AlignFrame>();
+ Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
try
{
SaveState(apanel, fileName, jout);
- String dssid = getDatasetIdRef(af.getViewport().getAlignment().getDataset());
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
if (!dsses.containsKey(dssid))
{
dsses.put(dssid, af);
}
}
- writeDatasetFor(dsses, ""+jout.hashCode()+" "+uniqueSetSuffix, jout);
-
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
try
{
jout.flush();
int ap, apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- Hashtable<String,AlignFrame> dsses = new Hashtable<String,AlignFrame>();
+ Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
jfileName = jfileName + ".xml";
}
SaveState(apanel, jfileName, jout);
- String dssid = getDatasetIdRef(af.getViewport().getAlignment().getDataset());
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
if (!dsses.containsKey(dssid))
{
dsses.put(dssid, af);
String fileName, JarOutputStream jout)
{
- for (String dssids:dsses.keySet())
+ for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = fileName + " Dataset for "+ _af.getTitle();
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
public JalviewModel SaveState(AlignmentPanel ap, String fileName,
JarOutputStream jout)
{
- return SaveState(ap, fileName, false,jout);
+ return SaveState(ap, fileName, false, jout);
}
+
/**
- * create a JalviewModel from an algnment view and marshall it to a
- * JarOutputStream
- *
- * @param ap
- * panel to create jalview model for
- * @param fileName
- * name of alignment panel written to output stream
- * @param storeDS
- * when true, only write the dataset for the alignment, not the data associated with the view.
- * @param jout
- * jar output stream
- * @param out
- * jar entry name
- */
- public JalviewModel SaveState(AlignmentPanel ap, String fileName, boolean storeDS,
- JarOutputStream jout)
+ * create a JalviewModel from an algnment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param storeDS
+ * when true, only write the dataset for the alignment, not the data
+ * associated with the view.
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
+ */
+ public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ boolean storeDS, JarOutputStream jout)
{
initSeqRefs();
Vector jmolViewIds = new Vector(); //
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getDefault("VERSION","Development Build"));
+ object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+ "Development Build"));
jalview.datamodel.AlignmentI jal = av.getAlignment();
// SAVE SEQUENCES
String id = "";
- jalview.datamodel.SequenceI jds,jdatasq;
+ jalview.datamodel.SequenceI jds, jdatasq;
for (int i = 0; i < jal.getHeight(); i++)
{
jds = jal.getSequenceAt(i);
- jdatasq=jds.getDatasetSequence() == null ? jds : jds.getDatasetSequence();
+ jdatasq = jds.getDatasetSequence() == null ? jds : jds
+ .getDatasetSequence();
id = seqHash(jds);
if (seqRefIds.get(id) != null)
IdentityHashMap groupRefs = new IdentityHashMap();
if (storeDS)
{
- for (SequenceI sq:jal.getSequences())
+ for (SequenceI sq : jal.getSequences())
+ {
+ // Store annotation on dataset sequences only
+ jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
{
- // Store annotation on dataset sequences only
- jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
- if (aa!=null && aa.length>0)
- {
- storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
- vamsasSet);
- }
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
- } else {
+ }
+ }
+ else
+ {
if (jal.getAlignmentAnnotation() != null)
{
// Store the annotation shown on the alignment.
}
else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
{
- groups[i]
- .setColour(ColourSchemeProperty
- .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
- .getBaseColour()));
+ groups[i].setColour("AnnotationColourGradient");
+ groups[i].setAnnotationColours(constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) sg.cs,
+ userColours, jms));
}
else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
}
else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
{
- jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
- .getGlobalColourScheme();
+ AnnotationColours ac = constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme(),
+ userColours, jms);
- AnnotationColours ac = new AnnotationColours();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
- {
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
- userColours, jms));
- }
- else
- {
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
- }
-
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- ac.setPerSequence(acg.isSeqAssociated());
- ac.setPredefinedColours(acg.isPredefinedColours());
view.setAnnotationColours(ac);
view.setBgColour("AnnotationColourGradient");
}
return object;
}
- private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, IdentityHashMap groupRefs, AlignmentViewport av, Set<String> calcIdSet, boolean storeDS, SequenceSet vamsasSet)
+ private AnnotationColours constructAnnotationColours(
+ AnnotationColourGradient acg, Vector userColours,
+ JalviewModelSequence jms)
+ {
+ AnnotationColours ac = new AnnotationColours();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ ac.setAnnotation(acg.getAnnotation());
+ if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ {
+ ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ userColours, jms));
+ }
+ else
+ {
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg
+ .getBaseColour()));
+ }
+
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ ac.setPerSequence(acg.isSeqAssociated());
+ ac.setPredefinedColours(acg.isPredefinedColours());
+ return ac;
+ }
+
+ private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
+ IdentityHashMap groupRefs, AlignmentViewport av,
+ Set<String> calcIdSet, boolean storeDS, SequenceSet vamsasSet)
{
for (int i = 0; i < aa.length; i++)
}
if (!storeDS || (storeDS && !aa[i].autoCalculated))
{
- // skip autocalculated annotation - these are only provided for alignments
+ // skip autocalculated annotation - these are only provided for
+ // alignments
vamsasSet.addAnnotation(an);
}
}
-
+
}
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers=new Vector<AppJmol>();
+ newStructureViewers = new Vector<AppJmol>();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
af = LoadJalviewAlign(jprovider);
-
+
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
reportErrors();
- }
- finally {
+ } finally
+ {
try
{
SwingUtilities.invokeAndWait(new Runnable()
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af= null,_af = null;
+ jalview.gui.AlignFrame af = null, _af = null;
Hashtable gatherToThisFrame = new Hashtable();
final String file = jprovider.getFilename();
try
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = (jms.getViewportCount()>0) ? jms.getViewport(0) : null;
-
+ Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ : null;
+
// ////////////////////////////////
// LOAD SEQUENCES
}
}
}
-
// ///////////////////////
// LOAD GROUPS
// Create alignment markup and styles for this view
if (jms.getJGroupCount() > 0)
{
JGroup[] groups = jms.getJGroup();
-
+ boolean addAnnotSchemeGroup = false;
for (int i = 0; i < groups.length; i++)
{
ColourSchemeI cs = null;
{
cs = GetUserColourScheme(jms, groups[i].getColour());
}
+ else if (groups[i].getColour().equals("AnnotationColourGradient")
+ && groups[i].getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ cs = null;
+ }
else
{
cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
}
}
al.addGroup(sg);
-
+ if (addAnnotSchemeGroup)
+ {
+ // reconstruct the annotation colourscheme
+ sg.cs = constructAnnotationColour(
+ groups[i].getAnnotationColours(), null, al, jms, false);
+ }
}
}
- if (view==null)
+ if (view == null)
{
// only dataset in this model, so just return.
return null;
}
}
+ /**
+ * indicate that annotation colours are applied across all groups (pre
+ * Jalview 2.8.1 behaviour)
+ */
+ boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
+ object.getVersion());
+
AlignmentPanel ap = null;
boolean isnewview = true;
if (viewId != null)
// and finally return.
return af;
}
- Vector<AppJmol> newStructureViewers=null;
+
+ /**
+ *
+ * @param supported - minimum version we are comparing against
+ * @param version - version of data being processsed.
+ * @return true if version is development/null or evaluates to the same or
+ * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+ */
+ private boolean isVersionStringLaterThan(String supported, String version)
+ {
+ if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ || version.equalsIgnoreCase("Test"))
+ {
+ System.err.println("Assuming project file with "
+ + (version == null ? "null" : version)
+ + " is compatible with Jalview version " + supported);
+ return true;
+ }
+ else
+ {
+ StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
+ version, ".");
+ while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
+ {
+ // convert b to decimal to catch bugfix releases within a series
+ String curT = currentV.nextToken().toLowerCase().replace('b', '.');
+ String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
+ try
+ {
+ if (Float.valueOf(curT) > Float.valueOf(fileT))
+ {
+ // current version is newer than the version that wrote the file
+ return false;
+ }
+ } catch (NumberFormatException nfe)
+ {
+ System.err
+ .println("** WARNING: Version comparison failed for tokens ("
+ + curT
+ + ") and ("
+ + fileT
+ + ")\n** Current: '"
+ + supported + "' and Version: '" + version + "'");
+ }
+ }
+ if (currentV.hasMoreElements())
+ {
+ // fileV has no minor version but identical series to current
+ return false;
+ }
+ }
+ return true;
+ }
+
+ Vector<AppJmol> newStructureViewers = null;
+
protected void addNewStructureViewer(AppJmol sview)
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
sview.jmb.setFinishedLoadingFromArchive(false);
newStructureViewers.add(sview);
}
}
+
protected void setLoadingFinishedForNewStructureViewers()
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
- for (AppJmol sview:newStructureViewers)
+ for (AppJmol sview : newStructureViewers)
{
sview.jmb.setFinishedLoadingFromArchive(true);
}
newStructureViewers.clear();
- newStructureViewers=null;
+ newStructureViewers = null;
}
}
}
else if (view.getBgColour().startsWith("Annotation"))
{
- // int find annotation
- if (af.viewport.getAlignment().getAlignmentAnnotation() != null)
- {
- for (int i = 0; i < af.viewport.getAlignment()
- .getAlignmentAnnotation().length; i++)
- {
- if (af.viewport.getAlignment().getAlignmentAnnotation()[i].label
- .equals(view.getAnnotationColours().getAnnotation()))
- {
- if (af.viewport.getAlignment().getAlignmentAnnotation()[i]
- .getThreshold() == null)
- {
- af.viewport.getAlignment().getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(view
- .getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
-
- );
- }
+ AnnotationColours viewAnnColour = view.getAnnotationColours();
+ cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
- if (view.getAnnotationColours().getColourScheme()
- .equals("None"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours()
- .getMinColour()), new java.awt.Color(view
- .getAnnotationColours().getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme()
- .startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- {
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg = al.getGroups()
- .get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
+ // annpos
- /*
- * if
- * (view.getAnnotationColours().getColourScheme().equals("None"
- * )) { sg.cs = new AnnotationColourGradient(
- * af.viewport.getAlignment().getAlignmentAnnotation()[i], new
- * java.awt.Color(view.getAnnotationColours().
- * getMinColour()), new
- * java.awt.Color(view.getAnnotationColours().
- * getMaxColour()),
- * view.getAnnotationColours().getAboveThreshold()); } else
- */
- {
- sg.cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- sg.cs, view.getAnnotationColours()
- .getAboveThreshold());
- if (cs instanceof AnnotationColourGradient)
- {
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- }
- }
-
- }
- }
-
- break;
- }
-
- }
- }
}
else
{
return af;
}
+ private ColourSchemeI constructAnnotationColour(
+ AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+ JalviewModelSequence jms, boolean checkGroupAnnColour)
+ {
+ boolean propagateAnnColour = false;
+ ColourSchemeI cs = null;
+ AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
+ if (checkGroupAnnColour && al.getGroups() != null
+ && al.getGroups().size() > 0)
+ {
+ // pre 2.8.1 behaviour
+ // check to see if we should transfer annotation colours
+ propagateAnnColour = true;
+ for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+ {
+ if (sg.cs instanceof AnnotationColourGradient)
+ {
+ propagateAnnColour = false;
+ }
+ }
+ }
+ // int find annotation
+ if (annAlignment.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].label
+ .equals(viewAnnColour.getAnnotation()))
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
+ {
+ annAlignment.getAlignmentAnnotation()[i]
+ .setThreshold(new jalview.datamodel.GraphLine(
+ viewAnnColour.getThreshold(), "Threshold",
+ java.awt.Color.black)
+
+ );
+ }
+
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ new java.awt.Color(viewAnnColour.getMinColour()),
+ new java.awt.Color(viewAnnColour.getMaxColour()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ GetUserColourScheme(jms,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ ColourSchemeProperty.getColour(al,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
+ .isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
+
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ /*
+ * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+ * new AnnotationColourGradient(
+ * annAlignment.getAlignmentAnnotation()[i], new
+ * java.awt.Color(viewAnnColour. getMinColour()), new
+ * java.awt.Color(viewAnnColour. getMaxColour()),
+ * viewAnnColour.getAboveThreshold()); } else
+ */
+ {
+ sg.cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i], sg.cs,
+ viewAnnColour.getAboveThreshold());
+ if (cs instanceof AnnotationColourGradient)
+ {
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs)
+ .setSeqAssociated(viewAnnColour.isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ }
+ }
+
+ }
+ }
+
+ break;
+ }
+
+ }
+ }
+ return cs;
+ }
+
private void reorderAutoannotation(AlignFrame af, Alignment al,
ArrayList<JvAnnotRow> autoAlan)
{
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
// and update the current dataset alignment
- if (ds==null) {
- if (dseqs!=null) {
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
if (!dseqs.contains(dsq))
{
dseqs.add(dsq);
}
- } else {
- if (ds.findIndex(dsq)<0)
+ }
+ else
+ {
+ if (ds.findIndex(dsq) < 0)
{
ds.addSequence(dsq);
}
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
- System.err.println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
+ System.err
+ .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println((System.currentTimeMillis()-start));
}
}
float value = slider.getValue();
-
+ List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.remove(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.add(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
-
}
-
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
}
/**
return;
}
- ColourSchemeI toChange = null;
- List<SequenceGroup> allGroups = null;
- int groupIndex = 0;
+ ColourSchemeI toChange = cs;
+ Iterator<SequenceGroup> allGroups = null;
if (allGroupsCheck.isSelected())
{
- allGroups = ap.av.getAlignment().getGroups();
- groupIndex = allGroups.size() - 1;
- }
- else
- {
- toChange = cs;
+ allGroups = ap.av.getAlignment().getGroups().listIterator();
}
- while (groupIndex > -1)
+ while (toChange != null)
{
- if (allGroups != null)
- {
- toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
-
- if (toChange == null)
- {
- groupIndex--;
-
- continue;
- }
- }
-
if (forConservation)
{
- if (toChange.conservationApplied())
- {
- toChange.setConservationInc(i);
- }
+ toChange.setConservationInc(i);
}
else
{
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
-
- groupIndex--;
+ if (allGroups != null && allGroups.hasNext())
+ {
+ while ((toChange = allGroups.next().cs) == null
+ && allGroups.hasNext())
+ ;
+ }
+ else
+ {
+ toChange = null;
+ }
}
ap.seqPanel.seqCanvas.repaint();
RenderingHints.VALUE_ANTIALIAS_ON);
g2.setColor(Color.white);
g2.fillRect(0, 0, width, height);
-
g2.setFont(font);
+ if (longestName==null || tree ==null)
+ {
+ g2.drawString("Calculating tree.",20,20);
+ }
offy = font.getSize() + 10;
fm = g2.getFontMetrics(font);
-#Fri Apr 25 13:56:18 BST 2014
+#Thu May 01 17:34:18 BST 2014
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor
jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor
jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor
+jalview.schemabinding.version2.AnnotationColourScheme=jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor
jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor
jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor
--- /dev/null
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class AnnotationColourScheme.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AnnotationColourScheme implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _aboveThreshold.
+ */
+ private int _aboveThreshold;
+
+ /**
+ * keeps track of state for field: _aboveThreshold
+ */
+ private boolean _has_aboveThreshold;
+
+ /**
+ * Field _annotation.
+ */
+ private java.lang.String _annotation;
+
+ /**
+ * Field _minColour.
+ */
+ private int _minColour;
+
+ /**
+ * keeps track of state for field: _minColour
+ */
+ private boolean _has_minColour;
+
+ /**
+ * Field _maxColour.
+ */
+ private int _maxColour;
+
+ /**
+ * keeps track of state for field: _maxColour
+ */
+ private boolean _has_maxColour;
+
+ /**
+ * Field _colourScheme.
+ */
+ private java.lang.String _colourScheme;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _perSequence.
+ */
+ private boolean _perSequence;
+
+ /**
+ * keeps track of state for field: _perSequence
+ */
+ private boolean _has_perSequence;
+
+ /**
+ * Field _predefinedColours.
+ */
+ private boolean _predefinedColours;
+
+ /**
+ * keeps track of state for field: _predefinedColours
+ */
+ private boolean _has_predefinedColours;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColourScheme()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAboveThreshold()
+ {
+ this._has_aboveThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteMaxColour()
+ {
+ this._has_maxColour = false;
+ }
+
+ /**
+ */
+ public void deleteMinColour()
+ {
+ this._has_minColour = false;
+ }
+
+ /**
+ */
+ public void deletePerSequence()
+ {
+ this._has_perSequence = false;
+ }
+
+ /**
+ */
+ public void deletePredefinedColours()
+ {
+ this._has_predefinedColours = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ * Returns the value of field 'aboveThreshold'.
+ *
+ * @return the value of field 'AboveThreshold'.
+ */
+ public int getAboveThreshold()
+ {
+ return this._aboveThreshold;
+ }
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public java.lang.String getAnnotation()
+ {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'colourScheme'.
+ *
+ * @return the value of field 'ColourScheme'.
+ */
+ public java.lang.String getColourScheme()
+ {
+ return this._colourScheme;
+ }
+
+ /**
+ * Returns the value of field 'maxColour'.
+ *
+ * @return the value of field 'MaxColour'.
+ */
+ public int getMaxColour()
+ {
+ return this._maxColour;
+ }
+
+ /**
+ * Returns the value of field 'minColour'.
+ *
+ * @return the value of field 'MinColour'.
+ */
+ public int getMinColour()
+ {
+ return this._minColour;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean getPerSequence()
+ {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean getPredefinedColours()
+ {
+ return this._predefinedColours;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAboveThreshold.
+ *
+ * @return true if at least one AboveThreshold has been added
+ */
+ public boolean hasAboveThreshold()
+ {
+ return this._has_aboveThreshold;
+ }
+
+ /**
+ * Method hasMaxColour.
+ *
+ * @return true if at least one MaxColour has been added
+ */
+ public boolean hasMaxColour()
+ {
+ return this._has_maxColour;
+ }
+
+ /**
+ * Method hasMinColour.
+ *
+ * @return true if at least one MinColour has been added
+ */
+ public boolean hasMinColour()
+ {
+ return this._has_minColour;
+ }
+
+ /**
+ * Method hasPerSequence.
+ *
+ * @return true if at least one PerSequence has been added
+ */
+ public boolean hasPerSequence()
+ {
+ return this._has_perSequence;
+ }
+
+ /**
+ * Method hasPredefinedColours.
+ *
+ * @return true if at least one PredefinedColours has been added
+ */
+ public boolean hasPredefinedColours()
+ {
+ return this._has_predefinedColours;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean isPerSequence()
+ {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean isPredefinedColours()
+ {
+ return this._predefinedColours;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'aboveThreshold'.
+ *
+ * @param aboveThreshold
+ * the value of field 'aboveThreshold'.
+ */
+ public void setAboveThreshold(final int aboveThreshold)
+ {
+ this._aboveThreshold = aboveThreshold;
+ this._has_aboveThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation
+ * the value of field 'annotation'.
+ */
+ public void setAnnotation(final java.lang.String annotation)
+ {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'colourScheme'.
+ *
+ * @param colourScheme
+ * the value of field 'colourScheme'.
+ */
+ public void setColourScheme(final java.lang.String colourScheme)
+ {
+ this._colourScheme = colourScheme;
+ }
+
+ /**
+ * Sets the value of field 'maxColour'.
+ *
+ * @param maxColour
+ * the value of field 'maxColour'.
+ */
+ public void setMaxColour(final int maxColour)
+ {
+ this._maxColour = maxColour;
+ this._has_maxColour = true;
+ }
+
+ /**
+ * Sets the value of field 'minColour'.
+ *
+ * @param minColour
+ * the value of field 'minColour'.
+ */
+ public void setMinColour(final int minColour)
+ {
+ this._minColour = minColour;
+ this._has_minColour = true;
+ }
+
+ /**
+ * Sets the value of field 'perSequence'.
+ *
+ * @param perSequence
+ * the value of field 'perSequence'.
+ */
+ public void setPerSequence(final boolean perSequence)
+ {
+ this._perSequence = perSequence;
+ this._has_perSequence = true;
+ }
+
+ /**
+ * Sets the value of field 'predefinedColours'.
+ *
+ * @param predefinedColours
+ * the value of field 'predefinedColours'.
+ */
+ public void setPredefinedColours(final boolean predefinedColours)
+ {
+ this._predefinedColours = predefinedColours;
+ this._has_predefinedColours = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.AnnotationColourScheme
+ */
+ public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.AnnotationColourScheme.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
*
* @version $Revision$ $Date$
*/
-public class AnnotationColours implements java.io.Serializable
+public class AnnotationColours extends AnnotationColourScheme implements
+ java.io.Serializable
{
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _aboveThreshold.
- */
- private int _aboveThreshold;
-
- /**
- * keeps track of state for field: _aboveThreshold
- */
- private boolean _has_aboveThreshold;
-
- /**
- * Field _annotation.
- */
- private java.lang.String _annotation;
-
- /**
- * Field _minColour.
- */
- private int _minColour;
-
- /**
- * keeps track of state for field: _minColour
- */
- private boolean _has_minColour;
-
- /**
- * Field _maxColour.
- */
- private int _maxColour;
-
- /**
- * keeps track of state for field: _maxColour
- */
- private boolean _has_maxColour;
-
- /**
- * Field _colourScheme.
- */
- private java.lang.String _colourScheme;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _perSequence.
- */
- private boolean _perSequence;
-
- /**
- * keeps track of state for field: _perSequence
- */
- private boolean _has_perSequence;
-
- /**
- * Field _predefinedColours.
- */
- private boolean _predefinedColours;
-
- /**
- * keeps track of state for field: _predefinedColours
- */
- private boolean _has_predefinedColours;
-
// ----------------/
// - Constructors -/
// ----------------/
// -----------/
/**
- */
- public void deleteAboveThreshold()
- {
- this._has_aboveThreshold = false;
- }
-
- /**
- */
- public void deleteMaxColour()
- {
- this._has_maxColour = false;
- }
-
- /**
- */
- public void deleteMinColour()
- {
- this._has_minColour = false;
- }
-
- /**
- */
- public void deletePerSequence()
- {
- this._has_perSequence = false;
- }
-
- /**
- */
- public void deletePredefinedColours()
- {
- this._has_predefinedColours = false;
- }
-
- /**
- */
- public void deleteThreshold()
- {
- this._has_threshold = false;
- }
-
- /**
- * Returns the value of field 'aboveThreshold'.
- *
- * @return the value of field 'AboveThreshold'.
- */
- public int getAboveThreshold()
- {
- return this._aboveThreshold;
- }
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return the value of field 'Annotation'.
- */
- public java.lang.String getAnnotation()
- {
- return this._annotation;
- }
-
- /**
- * Returns the value of field 'colourScheme'.
- *
- * @return the value of field 'ColourScheme'.
- */
- public java.lang.String getColourScheme()
- {
- return this._colourScheme;
- }
-
- /**
- * Returns the value of field 'maxColour'.
- *
- * @return the value of field 'MaxColour'.
- */
- public int getMaxColour()
- {
- return this._maxColour;
- }
-
- /**
- * Returns the value of field 'minColour'.
- *
- * @return the value of field 'MinColour'.
- */
- public int getMinColour()
- {
- return this._minColour;
- }
-
- /**
- * Returns the value of field 'perSequence'.
- *
- * @return the value of field 'PerSequence'.
- */
- public boolean getPerSequence()
- {
- return this._perSequence;
- }
-
- /**
- * Returns the value of field 'predefinedColours'.
- *
- * @return the value of field 'PredefinedColours'.
- */
- public boolean getPredefinedColours()
- {
- return this._predefinedColours;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- }
-
- /**
- * Method hasAboveThreshold.
- *
- * @return true if at least one AboveThreshold has been added
- */
- public boolean hasAboveThreshold()
- {
- return this._has_aboveThreshold;
- }
-
- /**
- * Method hasMaxColour.
- *
- * @return true if at least one MaxColour has been added
- */
- public boolean hasMaxColour()
- {
- return this._has_maxColour;
- }
-
- /**
- * Method hasMinColour.
- *
- * @return true if at least one MinColour has been added
- */
- public boolean hasMinColour()
- {
- return this._has_minColour;
- }
-
- /**
- * Method hasPerSequence.
- *
- * @return true if at least one PerSequence has been added
- */
- public boolean hasPerSequence()
- {
- return this._has_perSequence;
- }
-
- /**
- * Method hasPredefinedColours.
- *
- * @return true if at least one PredefinedColours has been added
- */
- public boolean hasPredefinedColours()
- {
- return this._has_predefinedColours;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- }
-
- /**
- * Returns the value of field 'perSequence'.
- *
- * @return the value of field 'PerSequence'.
- */
- public boolean isPerSequence()
- {
- return this._perSequence;
- }
-
- /**
- * Returns the value of field 'predefinedColours'.
- *
- * @return the value of field 'PredefinedColours'.
- */
- public boolean isPredefinedColours()
- {
- return this._predefinedColours;
- }
-
- /**
* Method isValid.
*
* @return true if this object is valid according to the schema
}
/**
- * Sets the value of field 'aboveThreshold'.
- *
- * @param aboveThreshold
- * the value of field 'aboveThreshold'.
- */
- public void setAboveThreshold(final int aboveThreshold)
- {
- this._aboveThreshold = aboveThreshold;
- this._has_aboveThreshold = true;
- }
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation
- * the value of field 'annotation'.
- */
- public void setAnnotation(final java.lang.String annotation)
- {
- this._annotation = annotation;
- }
-
- /**
- * Sets the value of field 'colourScheme'.
- *
- * @param colourScheme
- * the value of field 'colourScheme'.
- */
- public void setColourScheme(final java.lang.String colourScheme)
- {
- this._colourScheme = colourScheme;
- }
-
- /**
- * Sets the value of field 'maxColour'.
- *
- * @param maxColour
- * the value of field 'maxColour'.
- */
- public void setMaxColour(final int maxColour)
- {
- this._maxColour = maxColour;
- this._has_maxColour = true;
- }
-
- /**
- * Sets the value of field 'minColour'.
- *
- * @param minColour
- * the value of field 'minColour'.
- */
- public void setMinColour(final int minColour)
- {
- this._minColour = minColour;
- this._has_minColour = true;
- }
-
- /**
- * Sets the value of field 'perSequence'.
- *
- * @param perSequence
- * the value of field 'perSequence'.
- */
- public void setPerSequence(final boolean perSequence)
- {
- this._perSequence = perSequence;
- this._has_perSequence = true;
- }
-
- /**
- * Sets the value of field 'predefinedColours'.
- *
- * @param predefinedColours
- * the value of field 'predefinedColours'.
- */
- public void setPredefinedColours(final boolean predefinedColours)
- {
- this._predefinedColours = predefinedColours;
- this._has_predefinedColours = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold
- * the value of field 'threshold'.
- */
- public void setThreshold(final float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
* Method unmarshal.
*
* @param reader
* marshaling
* @throws org.exolab.castor.xml.ValidationException
* if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.AnnotationColours
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.AnnotationColourScheme
*/
- public static jalview.schemabinding.version2.AnnotationColours unmarshal(
+ public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller
+ return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
.unmarshal(
jalview.schemabinding.version2.AnnotationColours.class,
reader);
*/
private java.util.Vector _seqList;
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
// ----------------/
// - Constructors -/
// ----------------/
}
/**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+ {
+ return this._annotationColours;
+ }
+
+ /**
* Returns the value of field 'colour'.
*
* @return the value of field 'Colour'.
}
/**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours
+ * the value of field 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)
+ {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
* Sets the value of field 'colour'.
*
* @param colour
--- /dev/null
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.AnnotationColourScheme;
+
+/**
+ * Class AnnotationColourSchemeDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AnnotationColourSchemeDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColourSchemeDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "AnnotationColourScheme";
+ _elementDefinition = false;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _aboveThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasAboveThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getAboveThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteAboveThreshold();
+ return;
+ }
+ target.setAboveThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _aboveThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _annotation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_annotation", "annotation",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ return target.getAnnotation();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ target.setAnnotation((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _minColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_minColour", "minColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasMinColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getMinColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMinColour();
+ return;
+ }
+ target.setMinColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _minColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _maxColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_maxColour", "maxColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasMaxColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getMaxColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMaxColour();
+ return;
+ }
+ target.setMaxColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _maxColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colourScheme
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_colourScheme", "colourScheme",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ return target.getColourScheme();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ target.setColourScheme((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colourScheme
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_threshold", "threshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _threshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _perSequence
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_perSequence", "perSequence",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasPerSequence())
+ {
+ return null;
+ }
+ return (target.getPerSequence() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePerSequence();
+ return;
+ }
+ target.setPerSequence(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _perSequence
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _predefinedColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_predefinedColours",
+ "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasPredefinedColours())
+ {
+ return null;
+ }
+ return (target.getPredefinedColours() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePredefinedColours();
+ return;
+ }
+ target.setPredefinedColours(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _predefinedColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AnnotationColourScheme.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
*
* @version $Revision$ $Date$
*/
-public class AnnotationColoursDescriptor extends
- org.exolab.castor.xml.util.XMLClassDescriptorImpl
+public class AnnotationColoursDescriptor
+ extends
+ jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
{
// --------------------------/
public AnnotationColoursDescriptor()
{
super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor());
_nsURI = "www.jalview.org";
_xmlName = "AnnotationColours";
_elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- // -- initialize attribute descriptors
-
- // -- _aboveThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasAboveThreshold())
- {
- return null;
- }
- return new java.lang.Integer(target.getAboveThreshold());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteAboveThreshold();
- return;
- }
- target.setAboveThreshold(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _aboveThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _annotation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_annotation", "annotation",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- return target.getAnnotation();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- target.setAnnotation((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _annotation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _minColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_minColour", "minColour",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasMinColour())
- {
- return null;
- }
- return new java.lang.Integer(target.getMinColour());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteMinColour();
- return;
- }
- target.setMinColour(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _minColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _maxColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_maxColour", "maxColour",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasMaxColour())
- {
- return null;
- }
- return new java.lang.Integer(target.getMaxColour());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteMaxColour();
- return;
- }
- target.setMaxColour(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _maxColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _colourScheme
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_colourScheme", "colourScheme",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- return target.getColourScheme();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- target.setColourScheme((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _colourScheme
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Float.TYPE, "_threshold", "threshold",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasThreshold())
- {
- return null;
- }
- return new java.lang.Float(target.getThreshold());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteThreshold();
- return;
- }
- target.setThreshold(((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _threshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
- }
- desc.setValidator(fieldValidator);
- // -- _perSequence
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_perSequence", "perSequence",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasPerSequence())
- {
- return null;
- }
- return (target.getPerSequence() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deletePerSequence();
- return;
- }
- target.setPerSequence(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _perSequence
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _predefinedColours
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_predefinedColours",
- "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasPredefinedColours())
- {
- return null;
- }
- return (target.getPredefinedColours() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deletePredefinedColours();
- return;
- }
- target.setPredefinedColours(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _predefinedColours
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- initialize element descriptors
-
}
// -----------/
typeValidator.setWhiteSpace("preserve");
}
desc.setValidator(fieldValidator);
+ // -- _annotationColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.AnnotationColours.class,
+ "_annotationColours", "annotationColours",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ return target.getAnnotationColours();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.AnnotationColours();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotationColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
}
// -----------/
*/
package jalview.schemes;
-import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Map;
-public class AnnotationColourGradient extends ResidueColourScheme
+public class AnnotationColourGradient extends FollowerColourScheme
{
public static final int NO_THRESHOLD = -1;
float r1, g1, b1, rr, gg, bb, dr, dg, db;
- ColourSchemeI colourScheme;
-
private boolean predefinedColours = false;
private boolean seqAssociated = false;
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
-
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+ acg.thresholdIsMinMax = thresholdIsMinMax;
+ acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+ acg.r1 = r1;
+ acg.g1 = g1;
+ acg.b1 = b1;
+ acg.rr = rr;
+ acg.gg = gg;
+ acg.bb = bb;
+ acg.dr = dr;
+ acg.dg = dg;
+ acg.db = db;
+ acg.predefinedColours = predefinedColours;
+ acg.seqAssociated = seqAssociated;
+
+ return acg;
+ }
/**
* Creates a new AnnotationColourGradient object.
*/
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- // TODO Auto-generated method stub
super.alignmentChanged(alignment, hiddenReps);
if (seqAssociated && annotation.getCalcId() != null)
{
seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
}
- for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+ // resolve the context containing all the annotation for the sequence
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+ for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
if (alan.sequenceRef != null
}
}
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
public Color getMinColour()
{
return new Color((int) r1, (int) g1, (int) b1);
{
seqAssociated = sassoc;
}
- @Override
- public void setConsensus(Hashtable[] consensus)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConsensus(consensus);
- }
- }
- @Override
- public void setConservation(Conservation cons)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConservation(cons);
- }
- }
- @Override
- public void setConservationInc(int i)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConservationInc(i);
- }
- }
}
import jalview.analysis.AAFrequency;
import java.awt.Color;
+import java.util.Map;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public class Blosum62ColourScheme extends ResidueColourScheme
return currentColour;
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
+ return newcs;
+ }
}
{
this.includeGaps = includeGaps;
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ClustalxColourScheme css= new ClustalxColourScheme(sg, hiddenRepSequences);
+ css.includeGaps = includeGaps;
+ return css;
+ }
}
class ConsensusColour
public interface ColourSchemeI
{
+ /**
+ *
+ * @param c
+ * @return the colour for the given character
+ */
public Color findColour(char c);
+ /**
+ *
+ * @param c - sequence symbol or gap
+ * @param j - position in seq
+ * @param seq - sequence being coloured
+ * @return context dependent colour for the given symbol at the position in the given sequence
+ */
public Color findColour(char c, int j, SequenceI seq);
+ /**
+ * assign the given consensus profile for the colourscheme
+ */
public void setConsensus(java.util.Hashtable[] h);
+ /**
+ * assign the given conservation to the colourscheme
+ * @param c
+ */
public void setConservation(jalview.analysis.Conservation c);
+ /**
+ * enable or disable conservation shading for this colourscheme
+ * @param conservationApplied
+ */
+ public void setConservationApplied(boolean conservationApplied);
+ /**
+ *
+ * @return true if conservation shading is enabled for this colourscheme
+ */
public boolean conservationApplied();
+ /**
+ * set scale factor for bleaching of colour in unconserved regions
+ * @param i
+ */
public void setConservationInc(int i);
+ /**
+ *
+ * @return scale factor for bleaching colour in unconserved regions
+ */
public int getConservationInc();
+ /**
+ *
+ * @return percentage identity threshold for applying colourscheme
+ */
public int getThreshold();
+ /**
+ * set percentage identity threshold and type of %age identity calculation for shading
+ * @param ct 0..100 percentage identity for applying this colourscheme
+ * @param ignoreGaps when true, calculate PID without including gapped positions
+ */
public void setThreshold(int ct, boolean ignoreGaps);
+ /**
+ * recalculate dependent data using the given sequence collection, taking account of hidden rows
+ * @param alignment
+ * @param hiddenReps
+ */
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps);
+ /**
+ * create a new instance of the colourscheme configured to colour the given connection
+ * @param sg
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transfered
+ */
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
}
--- /dev/null
+package jalview.schemes;
+
+import jalview.analysis.Conservation;
+
+import java.util.Hashtable;
+
+/**
+ * Colourscheme that takes its colours from some other colourscheme
+ * @author jimp
+ *
+ */
+public class FollowerColourScheme extends ResidueColourScheme
+{
+
+ protected ColourSchemeI colourScheme;
+
+ public ColourSchemeI getBaseColour()
+ {
+ return colourScheme;
+ }
+
+ @Override
+ public void setConsensus(Hashtable[] consensus)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConsensus(consensus);
+ }
+ }
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConservation(cons);
+ }
+ }
+
+ @Override
+ public void setConservationInc(int i)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConservationInc(i);
+ }
+ }
+
+}
{
return conservationColouring;
}
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
public void setConservationInc(int i)
{
{
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ try {
+ return getClass().newInstance();
+ }
+ catch (Exception q)
+ {
+ throw new Error("Serious implementation error: cannot duplicate colourscheme "+getClass().getName(), q);
+ }
+ }
}
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
int w = 0;
- for (AlignmentAnnotation al : alignment
+ for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
}
return cols[j];
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new TCoffeeColourScheme(sg);
+ }
}
package jalview.schemes;
import java.awt.Color;
+import java.util.Map;
import java.util.StringTokenizer;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public class UserColourScheme extends ResidueColourScheme
super(ResidueProperties.aaIndex);
colors = newColors;
}
-
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ UserColourScheme usc = new UserColourScheme(colors);
+ if (lowerCaseColours!=null) {
+ usc.schemeName = new String(schemeName);
+ usc.lowerCaseColours = new Color[lowerCaseColours.length];
+ System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0, lowerCaseColours.length);
+ }
+ return usc;
+ }
public UserColourScheme(String colour)
{
super(ResidueProperties.aaIndex);
public void parseAppletParameter(String paramValue)
{
+ // TODO: need a function to generate appletParameter colour string from a UCS
StringTokenizer st = new StringTokenizer(paramValue, ";");
StringTokenizer st2;
String token = null, colour, residues;
// calculation till later or to do all calculations in thread.
// via changecolour
globalColourScheme = cs;
+ boolean recalc=false;
+ if (cs!=null)
+ {
+ cs.setConservationApplied(recalc = getConservationSelected());
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme)
+ {
+ recalc = true;
+ cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+ } else {
+ cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+ }
+ if (recalc)
+ {
+ cs.setConsensus(hconsensus);
+ cs.setConservation(hconservation);
+ }
+ cs.alignmentChanged(alignment, hiddenRepSequences);
+ }
if (getColourAppliesToAllGroups())
{
for (SequenceGroup sg : getAlignment().getGroups())
sg.cs = null;
continue;
}
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(sg, getHiddenRepSequences());
- }
- else
- {
- try
- {
- sg.cs = cs.getClass().newInstance();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- sg.cs = cs;
- }
- }
-
+ sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.setConsPercGaps(ConsPercGaps);
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(getHiddenRepSequences()), 0,
- sg.getWidth()));
+ recalc=true;
}
else
{
if (getConservationSelected())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(getHiddenRepSequences()), 0,
- getAlignment().getWidth() - 1);
- c.calculate();
- c.verdict(false, getConsPercGaps());
- sg.cs.setConservation(c);
+ sg.cs.setConservationApplied(true);
+ recalc=true;
}
else
{
sg.cs.setConservation(null);
- sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+ if (recalc) {
+ sg.recalcConservation();
+ } else {
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
}
-
}
}
* view
*/
protected Hashtable[] hStrucConsensus = null;
-
+
+ protected Conservation hconservation = null;
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ hconservation = cons;
+ }
/**
* percentage gaps allowed in a column before all amino acid properties should
* be considered unconserved
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
- cs.alignmentChanged(alignment, null);
+ cs.alignmentChanged(alignment, hiddenRepSequences);
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
ourAnnot.add(conservation);
ourAnnot.add(quality);
ourAnnots = ourAnnot;
-
+ ConsPercGaps = alignViewport.getConsPercGaps();
// AlignViewport.UPDATING_CONSERVATION = true;
if (alignment == null || (alWidth = alignment.getWidth()) < 0)
{
if (b || !calcMan.isWorking(this) && cons != null
&& conservation != null && quality != null)
+ {
+ alignViewport.setConservation(cons);
cons.completeAnnotations(conservation, quality, 0, alWidth);
+ }
}
@Override
import static org.junit.Assert.*;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import java.io.File;
@AfterClass
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.quit();
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
}
public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
{
assertTrue("Didn't set T-coffee colourscheme for imported project.",af.getViewport().getGlobalColourScheme().getClass().equals(jalview.schemes.TCoffeeColourScheme.class));
System.out.println("T-Coffee score shading successfully recovered from project.");
}
+ @Test
+ public void testColourByAnnotScores() throws Exception
+ {
+ String inFile = "examples/uniref50.fa",inAnnot="examples/testdata/uniref50_iupred.jva";
+ String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file "+inFile, af!=null);
+ af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null,null);
+ AlignmentAnnotation[] aa = af.getViewport().getAlignment().getSequenceAt(0).getAnnotation("IUPredWS (Short)");
+ assertTrue("Didn't find any IUPred annotation to use to shade alignment.",aa!=null && aa.length>0);
+ AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
+ AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
+ cs.setSeqAssociated(true);
+ gcs.setSeqAssociated(true);
+ af.changeColour(cs);
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(57);
+ sg.setEndRes(92);
+ sg.cs = gcs;
+ af.getViewport().getAlignment().addGroup(sg);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
+ af.alignPanel.alignmentChanged();
+ assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af=null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af!=null);
+
+ // check for group and alignment colourschemes
+
+ ColourSchemeI _rcs=af.getViewport().getGlobalColourScheme();
+ ColourSchemeI _rgcs=af.getViewport().getAlignment().getGroups().get(0).cs;
+ assertTrue("Didn't recover global colourscheme",_rcs!=null);
+ assertTrue("Didn't recover annotation colour global scheme",_rcs instanceof AnnotationColourGradient);
+ AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
+ assertTrue("Annotation colourscheme wasn't sequence associated",__rcs.isSeqAssociated());
+
+
+ boolean diffseqcols=false,diffgseqcols=false;
+ SequenceI[] sqs=af.getViewport().getAlignment().getSequencesArray();
+ for (int p=0,pSize=af.getViewport().getAlignment().getWidth();p<pSize && (!diffseqcols || !diffgseqcols);p++)
+ {
+ if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0])!=_rcs.findColour(sqs[5].getCharAt(p), p, sqs[5]))
+ {
+ diffseqcols = true;
+ }
+ }
+ assertTrue("Got Different sequence colours", diffseqcols);
+ System.out.println("Per sequence colourscheme (Background) successfully applied and recovered.");
+
+ assertTrue("Didn't recover group colourscheme",_rgcs!=null);
+ assertTrue("Didn't recover annotation colour group colourscheme",_rgcs instanceof AnnotationColourGradient);
+ __rcs = (AnnotationColourGradient) _rgcs;
+ assertTrue("Group Annotation colourscheme wasn't sequence associated",__rcs.isSeqAssociated());
+
+ for (int p=0,pSize=af.getViewport().getAlignment().getWidth();p<pSize && (!diffseqcols || !diffgseqcols);p++)
+ {
+ if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1])!=_rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2]))
+ {
+ diffgseqcols = true;
+ }
+ }
+ assertTrue("Got Different group sequence colours", diffgseqcols);
+ System.out.println("Per sequence (Group) colourscheme successfully applied and recovered.");
+ }
}
git://source.jalview.org / jalview.git / commitdiff