import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.FeatureColour;
-import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.StringUtils;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.ws.jws2.Jws2Discoverer;
import java.util.jar.JarOutputStream;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
import org.exolab.castor.xml.Marshaller;
List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
AlignViewport av = ap.av;
+ ViewportRanges vpRanges = av.getRanges();
JalviewModel object = new JalviewModel();
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
// TODO: omit sequence features from each alignment view's XML dump if we
// are storing dataset
- if (jds.getSequenceFeatures() != null)
+ List<jalview.datamodel.SequenceFeature> sfs = jds
+ .getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
{
- jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
- int index = 0;
- while (index < sf.length)
- {
- Features features = new Features();
+ Features features = new Features();
- features.setBegin(sf[index].getBegin());
- features.setEnd(sf[index].getEnd());
- features.setDescription(sf[index].getDescription());
- features.setType(sf[index].getType());
- features.setFeatureGroup(sf[index].getFeatureGroup());
- features.setScore(sf[index].getScore());
- if (sf[index].links != null)
+ features.setBegin(sf.getBegin());
+ features.setEnd(sf.getEnd());
+ features.setDescription(sf.getDescription());
+ features.setType(sf.getType());
+ features.setFeatureGroup(sf.getFeatureGroup());
+ features.setScore(sf.getScore());
+ if (sf.links != null)
+ {
+ for (int l = 0; l < sf.links.size(); l++)
{
- for (int l = 0; l < sf[index].links.size(); l++)
- {
- OtherData keyValue = new OtherData();
- keyValue.setKey("LINK_" + l);
- keyValue.setValue(sf[index].links.elementAt(l).toString());
- features.addOtherData(keyValue);
- }
+ OtherData keyValue = new OtherData();
+ keyValue.setKey("LINK_" + l);
+ keyValue.setValue(sf.links.elementAt(l).toString());
+ features.addOtherData(keyValue);
}
- if (sf[index].otherDetails != null)
+ }
+ if (sf.otherDetails != null)
+ {
+ String key;
+ Iterator<String> keys = sf.otherDetails.keySet().iterator();
+ while (keys.hasNext())
{
- String key;
- Iterator<String> keys = sf[index].otherDetails.keySet()
- .iterator();
- while (keys.hasNext())
- {
- key = keys.next();
- OtherData keyValue = new OtherData();
- keyValue.setKey(key);
- keyValue.setValue(sf[index].otherDetails.get(key).toString());
- features.addOtherData(keyValue);
- }
+ key = keys.next();
+ OtherData keyValue = new OtherData();
+ keyValue.setKey(key);
+ keyValue.setValue(sf.otherDetails.get(key).toString());
+ features.addOtherData(keyValue);
}
-
- jseq.addFeatures(features);
- index++;
}
+
+ jseq.addFeatures(features);
}
if (jdatasq.getAllPDBEntries() != null)
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
tree.setCurrentTree((av.currentTree == tp.getTree()));
- tree.setNewick(tp.getTree().toString());
+ tree.setNewick(tp.getTree().print());
tree.setThreshold(tp.treeCanvas.threshold);
tree.setFitToWindow(tp.fitToWindow.getState());
// group has references so set its ID field
jGroup.setId(groupRefs.get(sg));
}
- if (sg.cs != null)
+ ColourSchemeI colourScheme = sg.getColourScheme();
+ if (colourScheme != null)
{
- if (sg.cs.conservationApplied())
+ ResidueShaderI groupColourScheme = sg
+ .getGroupColourScheme();
+ if (groupColourScheme.conservationApplied())
{
- jGroup.setConsThreshold(sg.cs.getConservationInc());
+ jGroup.setConsThreshold(groupColourScheme.getConservationInc());
- if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, jms));
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(colourScheme.getSchemeName());
}
}
- else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+ else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
{
jGroup.setColour("AnnotationColourGradient");
jGroup.setAnnotationColours(constructAnnotationColours(
- (jalview.schemes.AnnotationColourGradient) sg.cs,
+ (jalview.schemes.AnnotationColourGradient) colourScheme,
userColours, jms));
}
- else if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ else if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, jms));
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(colourScheme.getSchemeName());
}
- jGroup.setPidThreshold(sg.cs.getThreshold());
+ jGroup.setPidThreshold(groupColourScheme.getThreshold());
}
jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
view.setWidth(size.width);
view.setHeight(size.height);
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
+ view.setStartRes(vpRanges.getStartRes());
+ view.setStartSeq(vpRanges.getStartSeq());
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
.getGlobalColourScheme()));
}
+ ResidueShaderI vcs = av.getResidueShading();
ColourSchemeI cs = av.getGlobalColourScheme();
if (cs != null)
{
- if (cs.conservationApplied())
+ if (vcs.conservationApplied())
{
- view.setConsThreshold(cs.getConservationInc());
+ view.setConsThreshold(vcs.getConservationInc());
if (cs instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(cs, userColours, jms));
}
}
-
- if (cs instanceof ResidueColourScheme)
- {
- view.setPidThreshold(cs.getThreshold());
- }
+ view.setPidThreshold(vcs.getThreshold());
}
view.setConservationSelected(av.getConservationSelected());
if (av.hasHiddenColumns())
{
- if (av.getColumnSelection() == null
- || av.getColumnSelection().getHiddenColumns() == null)
+ jalview.datamodel.HiddenColumns hidden = av.getAlignment()
+ .getHiddenColumns();
+ if (hidden == null || hidden.getHiddenRegions() == null)
{
warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
else
{
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
+ for (int c = 0; c < hidden.getHiddenRegions()
.size(); c++)
{
- int[] region = av.getColumnSelection().getHiddenColumns()
+ int[] region = hidden.getHiddenRegions()
.get(c);
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
return matchedFile;
}
+ /**
+ * Populates the AnnotationColours xml for save. This captures the settings of
+ * the options in the 'Colour by Annotation' dialog.
+ *
+ * @param acg
+ * @param userColours
+ * @param jms
+ * @return
+ */
private AnnotationColours constructAnnotationColours(
AnnotationColourGradient acg, List<UserColourScheme> 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)
+ // 2.10.2 save annotationId (unique) not annotation label
+ ac.setAnnotation(acg.getAnnotation().annotationId);
+ if (acg.getBaseColour() instanceof UserColourScheme)
{
ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
userColours, jms));
}
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
}
ac.setMaxColour(acg.getMaxColour().getRGB());
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- finalErrorMessage, "Error "
- + (saving ? "saving" : "loading")
- + " Jalview file", JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane
+ .showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage, "Error "
+ + (saving ? "saving" : "loading")
+ + " Jalview file",
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
Features[] features = jseqs[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
- jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
- features[f].getType(), features[f].getDescription(),
- features[f].getStatus(), features[f].getBegin(),
- features[f].getEnd(), features[f].getFeatureGroup());
-
- sf.setScore(features[f].getScore());
+ SequenceFeature sf = new SequenceFeature(features[f].getType(),
+ features[f].getDescription(), features[f].getBegin(),
+ features[f].getEnd(), features[f].getScore(),
+ features[f].getFeatureGroup());
+ sf.setStatus(features[f].getStatus());
for (int od = 0; od < features[f].getOtherDataCount(); od++)
{
OtherData keyValue = features[f].getOtherData(od);
&& jGroup.getAnnotationColours() != null)
{
addAnnotSchemeGroup = true;
- cs = null;
}
else
{
- cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(jGroup.getPidThreshold(), true);
+ cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
}
}
+ int pidThreshold = jGroup.getPidThreshold();
Vector<SequenceI> seqs = new Vector<SequenceI>();
SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
-
+ sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+ sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold());
sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
sg.textColour = new java.awt.Color(jGroup.getTextCol1());
if (addAnnotSchemeGroup)
{
// reconstruct the annotation colourscheme
- sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
- null, al, jms, false);
+ sg.setColourScheme(constructAnnotationColour(
+ jGroup.getAnnotationColours(), null, al, jms, false));
}
}
}
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
- tp = af.ShowNewickTree(
+ tp = af.showNewickTree(
new jalview.io.NewickFile(tree.getNewick()),
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ af.viewport.setThreshold(view.getPidThreshold());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setIncrement(view.getConsThreshold());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(
af.viewport.setThresholdTextColour(view.getTextColThreshold());
af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
.isShowUnconserved() : false);
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+ af.viewport.getRanges().setStartRes(view.getStartRes());
+ // startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
// apply colourschemes
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.getSequenceConsensusHash());
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
}
af.viewport.setGlobalColourScheme(cs);
+ af.viewport.getResidueShading().setThreshold(
+ view.getPidThreshold(), true);
+ af.viewport.getResidueShading().setConsensus(
+ af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
if (view.getConservationSelected() && cs != null)
{
- cs.setConservationInc(view.getConsThreshold());
+ af.viewport.getResidueShading().setConservationInc(
+ view.getConsThreshold());
}
af.changeColour(cs);
return af;
}
+ /**
+ * Reads saved data to restore Colour by Annotation settings
+ *
+ * @param viewAnnColour
+ * @param af
+ * @param al
+ * @param jms
+ * @param checkGroupAnnColour
+ * @return
+ */
private ColourSchemeI constructAnnotationColour(
AnnotationColours viewAnnColour, AlignFrame af, AlignmentI 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())
+ for (SequenceGroup sg : al.getGroups())
{
- if (sg.cs instanceof AnnotationColourGradient)
+ if (sg.getColourScheme() instanceof AnnotationColourGradient)
{
propagateAnnColour = false;
}
}
}
- // int find annotation
- if (annAlignment.getAlignmentAnnotation() != null)
+
+ /*
+ * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
+ */
+ String annotationId = viewAnnColour.getAnnotation();
+ AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
+
+ /*
+ * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
+ */
+ if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null)
{
for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
{
- if (annAlignment.getAlignmentAnnotation()[i].label
- .equals(viewAnnColour.getAnnotation()))
+ if (annotationId
+ .equals(annAlignment.getAlignmentAnnotation()[i].label))
{
- 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;
- }
+ matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
+ break;
+ }
+ }
+ }
+ if (matchedAnnotation == null)
+ {
+ System.err.println("Failed to match annotation colour scheme for "
+ + annotationId);
+ return null;
+ }
+ if (matchedAnnotation.getThreshold() == null)
+ {
+ matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
+ "Threshold", Color.black));
+ }
- /*
- * 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());
- }
- }
- }
+ AnnotationColourGradient cs = null;
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation, new Color(
+ viewAnnColour.getMinColour()), new Color(
+ viewAnnColour.getMaxColour()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(
+ jms, viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation,
+ ColourSchemeProperty.getColourScheme(al,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
- }
- }
+ boolean perSequenceOnly = viewAnnColour.isPerSequence();
+ boolean useOriginalColours = viewAnnColour.isPredefinedColours();
+ cs.setSeqAssociated(perSequenceOnly);
+ cs.setPredefinedColours(useOriginalColours);
- break;
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ SequenceGroup sg = al.getGroups().get(g);
+ if (sg.getGroupColourScheme() == null)
+ {
+ continue;
}
+ AnnotationColourGradient groupScheme = new AnnotationColourGradient(
+ matchedAnnotation, sg.getColourScheme(),
+ viewAnnColour.getAboveThreshold());
+ sg.setColourScheme(groupScheme);
+ groupScheme.setSeqAssociated(perSequenceOnly);
+ groupScheme.setPredefinedColours(useOriginalColours);
}
}
return cs;
git://source.jalview.org / jalview.git / blobdiff