import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
+import jalview.analysis.AnnotationSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.util.jarInputStreamProvider;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.AlignmentViewport.AutoAnnotation;
import jalview.viewmodel.PCAModel;
import jalview.viewmodel.ViewportRanges;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import javax.xml.stream.XMLStreamReader;
/**
- * Write out the current jalview desktop state as a Jalview XML stream.
- *
- * Note: the vamsas objects referred to here are primitive versions of the
- * VAMSAS project schema elements - they are not the same and most likely never
- * will be :)
- *
- * @author $author$
- * @version $Revision: 1.134 $
+ * Provides methods to read in or write out the Jalview desktop state as a
+ * Jalview XML model, as one or more entries in a .jar archive. The jar file may
+ * include additional data file entries, such as
+ * <ul>
+ * <li>PDB structure data files</li>
+ * <li>session state for one or more Jmol, Chimera or Varna structure
+ * viewers</li>
+ * </ul>
*/
public class Jalview2XML
{
+ private static final String TRUE = "true";
+
+ private static final String FALSE = "false";
+
private static final String VIEWER_PREFIX = "viewer_";
private static final String RNA_PREFIX = "rna_";
view.setRenderGaps(av.isRenderGaps());
view.setShowAnnotation(av.isShowAnnotation());
view.setShowBoxes(av.getShowBoxes());
+ view.setShowAutocalcAbove(av.isShowAutocalculatedAbove());
+ view.setSortAnnotationsBy(av.getSortAnnotationsBy().name());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
view.setRightAlignIds(av.isRightAlignIds());
// ////////////////////////////////
// LOAD ANNOTATIONS
- List<JvAnnotRow> autoAlan = new ArrayList<>();
+ List<AlignmentAnnotation> addedAnnotation = new ArrayList<>();
/*
* store any annotations which forward reference a group's ID
* test if annotation is automatically calculated for this view only
*/
boolean autoForView = false;
- if (annotation.getLabel().equals("Quality")
- || annotation.getLabel().equals("Conservation")
- || annotation.getLabel().equals("Consensus"))
+ if (annotation.getLabel().equals(AutoAnnotation.QUALITY.label)
+ || annotation.getLabel()
+ .equals(AutoAnnotation.CONSERVATION.label)
+ || annotation.getLabel()
+ .equals(AutoAnnotation.CONSENSUS.label))
{
// Kludge for pre 2.5 projects which lacked the autocalculated flag
autoForView = true;
- // JAXB has no has() test; schema defaults value to false
- // if (!annotation.hasAutoCalculated())
- // {
- // annotation.setAutoCalculated(true);
- // }
}
if (autoForView || annotation.isAutoCalculated())
{
}
al.addAnnotation(jda);
-
+ addedAnnotation.add(jda);
continue;
}
// Construct new annotation from model.
}
}
}
- jalview.datamodel.AlignmentAnnotation jaa = null;
+
+ /*
+ * construct the Jalview AlignmentAnnotation, add to alignment
+ */
+ AlignmentAnnotation jaa = null;
if (annotation.isGraph())
{
jaa.autoCalculated = true; // means annotation will be marked for
// update at end of load.
}
- if (annotation.getGraphHeight() != null)
+ Integer graphHeight = annotation.getGraphHeight();
+ if (graphHeight != null)
{
- jaa.graphHeight = annotation.getGraphHeight().intValue();
+ jaa.graphHeight = graphHeight.intValue();
}
jaa.belowAlignment = annotation.isBelowAlignment();
jaa.setCalcId(annotation.getCalcId());
jaa.setProperty(prop.getName(), prop.getValue());
}
}
- if (jaa.autoCalculated)
+ if (!jaa.autoCalculated)
{
- autoAlan.add(new JvAnnotRow(i, jaa));
- }
- else
- // if (!autoForView)
- {
- // add autocalculated group annotation and any user created annotation
- // for the view
+ // TODO ensure Consensus etc is enabled if found in project?
+ /*
+ * add autocalculated group annotation and any user created annotation
+ * for the view
+ */
al.addAnnotation(jaa);
}
+ addedAnnotation.add(jaa);
}
}
// ///////////////////////
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al,
+ cs = ColourSchemeProperty.getColourScheme(null, al,
jGroup.getColour());
}
}
if (isnewview)
{
- af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
- uniqueSeqSetId, viewId, autoAlan);
+ Map<String, String> originalPreferences = null;
+ try
+ {
+ originalPreferences = setAutocalcPreferences(jalviewModel);
+ af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
+ uniqueSeqSetId, viewId);
+ } finally
+ {
+ restoreAutocalcPreferences(originalPreferences);
+ }
+
+ /*
+ * resort annotations to their order in the project
+ * (also sets height and visibility for autocalc'd annotation)
+ */
av = af.getViewport();
+ new AnnotationSorter(av).sort(addedAnnotation);
ap = af.alignPanel;
+ ap.adjustAnnotationHeight();
}
/*
}
/**
+ * Restores previously captured preferences (or deletes the preference if the
+ * map entry value is null)
+ *
+ * @param originalPreferences
+ */
+ private void restoreAutocalcPreferences(
+ Map<String, String> originalPreferences)
+ {
+ for (Entry<String, String> entry : originalPreferences.entrySet())
+ {
+ String key = entry.getKey();
+ String value = entry.getValue();
+ if (value == null)
+ {
+ Cache.removeProperty(key);
+ }
+ else
+ {
+ Cache.setProperty(key, value);
+ }
+ }
+ }
+
+ /**
+ * Inspects saved annotations and temporarily sets preferences for whether
+ * autocalculated annotations should be created for Conservation, Consensus,
+ * Quality, Occupancy. Returns a map containing the original values (which may
+ * be null if property is not set, or is set to null).
+ *
+ * @param jalviewModel
+ * @return
+ */
+ private Map<String, String> setAutocalcPreferences(
+ JalviewModel jalviewModel)
+ {
+ Map<String, String> original = Cache.getProperties(
+ AutoAnnotation.OCCUPANCY.preferenceKey,
+ AutoAnnotation.CONSERVATION.preferenceKey,
+ AutoAnnotation.QUALITY.preferenceKey,
+ AutoAnnotation.CONSENSUS.preferenceKey);
+
+ Cache.setProperty(AutoAnnotation.OCCUPANCY.preferenceKey, FALSE);
+ Cache.setProperty(AutoAnnotation.CONSERVATION.preferenceKey, FALSE);
+ Cache.setProperty(AutoAnnotation.QUALITY.preferenceKey, FALSE);
+ Cache.setProperty(AutoAnnotation.CONSENSUS.preferenceKey, FALSE);
+
+ List<SequenceSet> sequenceSet = jalviewModel.getVamsasModel()
+ .getSequenceSet();
+
+ /*
+ * expect sequenceSet to have just one entry
+ */
+ if (sequenceSet.size() != 1)
+ {
+ System.err.println(
+ "Unexpected sequenceSet size: " + sequenceSet.size());
+ return original;
+ }
+ List<Annotation> anns = sequenceSet.get(0).getAnnotation();
+ for (Annotation ann : anns)
+ {
+ if (ann.isAutoCalculated())
+ {
+ String label = ann.getLabel();
+ if (AutoAnnotation.CONSERVATION.label.equals(label))
+ {
+ Cache.setProperty(AutoAnnotation.CONSERVATION.preferenceKey,
+ TRUE);
+ }
+ else if (AutoAnnotation.QUALITY.label.equals(label))
+ {
+ Cache.setProperty(AutoAnnotation.QUALITY.preferenceKey, TRUE);
+ }
+ else if (AutoAnnotation.CONSENSUS.label.equals(label))
+ {
+ Cache.setProperty(AutoAnnotation.CONSENSUS.preferenceKey, TRUE);
+ }
+ else if (AutoAnnotation.OCCUPANCY.label.equals(label))
+ {
+ Cache.setProperty(AutoAnnotation.OCCUPANCY.preferenceKey, TRUE);
+ }
+ }
+ }
+ return original;
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
// TODO: verify 'associate with all views' works still
tp.getTreeCanvas().setViewport(av); // af.viewport;
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
- // FIXME: should we use safeBoolean here ?
- tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
}
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
warn("There was a problem recovering stored Newick tree: \n"
{
if (val.contains("e")) // eh? what can it be?
{
- if (val.trim().equals("true"))
+ if (val.trim().equals(TRUE))
{
val = "1";
}
AlignFrame loadViewport(String file, List<JSeq> JSEQ,
List<SequenceI> hiddenSeqs, AlignmentI al,
JalviewModel jm, Viewport view, String uniqueSeqSetId,
- String viewId, List<JvAnnotRow> autoAlan)
+ String viewId)
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(
- safeBoolean(view.isConservationSelected()));
+ viewport.setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
- viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
+ Boolean autocalcFirst = view.isShowAutocalcAbove();
+ if (autocalcFirst != null)
+ {
+ af.setShowAutoCalculatedAbove(autocalcFirst.booleanValue());
+ }
+ String sortBy = view.getSortAnnotationsBy();
+ if (sortBy != null)
+ {
+ try
+ {
+ viewport.setSortAnnotationsBy(
+ SequenceAnnotationOrder.valueOf(sortBy));
+ } catch (IllegalArgumentException e)
+ {
+ Cache.log.error(
+ "Invalid annotation sort specifier in project: " + sortBy);
+ }
+ }
+ viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
viewport.setShowText(safeBoolean(view.isShowText()));
-
viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+ view.getBgColour());
}
}
+ /*
+ * turn off 'alignment colour applies to all groups'
+ * while restoring global colour scheme
+ */
+ viewport.setColourAppliesToAllGroups(false);
viewport.setGlobalColourScheme(cs);
viewport.getResidueShading().setThreshold(pidThreshold,
view.isIgnoreGapsinConsensus());
viewport.getResidueShading()
.setConsensus(viewport.getSequenceConsensusHash());
- viewport.setColourAppliesToAllGroups(false);
-
if (safeBoolean(view.isConservationSelected()) && cs != null)
{
viewport.getResidueShading()
.setConservationInc(safeInt(view.getConsThreshold()));
}
-
af.changeColour(cs);
-
viewport.setColourAppliesToAllGroups(true);
viewport
float min = safeFloat(safeFloat(setting.getMin()));
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
- FeatureColourI gc = new FeatureColour(minColour, maxColour,
+ FeatureColourI gc = new FeatureColour(maxColour, minColour,
+ maxColour,
noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
safeInt(view.getWidth()), safeInt(view.getHeight()));
// recompute any autoannotation
af.alignPanel.updateAnnotation(false, true);
- reorderAutoannotation(af, al, autoAlan);
af.alignPanel.alignmentChanged();
}
else
else
{
cs = new AnnotationColourGradient(matchedAnnotation,
- ColourSchemeProperty.getColourScheme(al,
+ ColourSchemeProperty.getColourScheme(af.getViewport(), al,
viewAnnColour.getColourScheme()),
safeInt(viewAnnColour.getAboveThreshold()));
}
return cs;
}
- private void reorderAutoannotation(AlignFrame af, AlignmentI al,
- List<JvAnnotRow> autoAlan)
- {
- // copy over visualization settings for autocalculated annotation in the
- // view
- if (al.getAlignmentAnnotation() != null)
- {
- /**
- * Kludge for magic autoannotation names (see JAL-811)
- */
- String[] magicNames = new String[] { "Consensus", "Quality",
- "Conservation" };
- JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
- Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
- for (String nm : magicNames)
- {
- visan.put(nm, nullAnnot);
- }
- for (JvAnnotRow auan : autoAlan)
- {
- visan.put(auan.template.label
- + (auan.template.getCalcId() == null ? ""
- : "\t" + auan.template.getCalcId()),
- auan);
- }
- int hSize = al.getAlignmentAnnotation().length;
- List<JvAnnotRow> reorder = new ArrayList<>();
- // work through any autoCalculated annotation already on the view
- // removing it if it should be placed in a different location on the
- // annotation panel.
- List<String> remains = new ArrayList<>(visan.keySet());
- for (int h = 0; h < hSize; h++)
- {
- jalview.datamodel.AlignmentAnnotation jalan = al
- .getAlignmentAnnotation()[h];
- if (jalan.autoCalculated)
- {
- String k;
- JvAnnotRow valan = visan.get(k = jalan.label);
- if (jalan.getCalcId() != null)
- {
- valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
- }
-
- if (valan != null)
- {
- // delete the auto calculated row from the alignment
- al.deleteAnnotation(jalan, false);
- remains.remove(k);
- hSize--;
- h--;
- if (valan != nullAnnot)
- {
- if (jalan != valan.template)
- {
- // newly created autoannotation row instance
- // so keep a reference to the visible annotation row
- // and copy over all relevant attributes
- if (valan.template.graphHeight >= 0)
-
- {
- jalan.graphHeight = valan.template.graphHeight;
- }
- jalan.visible = valan.template.visible;
- }
- reorder.add(new JvAnnotRow(valan.order, jalan));
- }
- }
- }
- }
- // Add any (possibly stale) autocalculated rows that were not appended to
- // the view during construction
- for (String other : remains)
- {
- JvAnnotRow othera = visan.get(other);
- if (othera != nullAnnot && othera.template.getCalcId() != null
- && othera.template.getCalcId().length() > 0)
- {
- reorder.add(othera);
- }
- }
- // now put the automatic annotation in its correct place
- int s = 0, srt[] = new int[reorder.size()];
- JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
- for (JvAnnotRow jvar : reorder)
- {
- rws[s] = jvar;
- srt[s++] = jvar.order;
- }
- reorder.clear();
- jalview.util.QuickSort.sort(srt, rws);
- // and re-insert the annotation at its correct position
- for (JvAnnotRow jvar : rws)
- {
- al.addAnnotation(jvar.template, jvar.order);
- }
- af.alignPanel.adjustAnnotationHeight();
- }
- }
-
Hashtable skipList = null;
/**
noValueColour = maxcol;
}
- colour = new FeatureColour(mincol, maxcol, noValueColour,
+ colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
final List<String> attributeName = colourModel.getAttributeName();
git://source.jalview.org / jalview.git / blobdiff