for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.rightAlignIds);
+ view.setRightAlignIds(av.isRightAlignIds());
view.setShowSequenceFeatures(av.showSequenceFeatures);
view.setShowText(av.getShowText());
view.setShowUnconserved(av.getShowUnconserved());
view.setFollowHighlight(av.followHighlight);
view.setFollowSelection(av.followSelection);
view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
- if (av.featuresDisplayed != null)
+ if (av.getFeaturesDisplayed() != null)
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+ String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder;
Vector settingsAdded = new Vector();
Object gstyle = null;
{
for (int ro = 0; ro < renderOrder.length; ro++)
{
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getFeatureStyle(renderOrder[ro]);
Setting setting = new Setting();
setting.setType(renderOrder[ro]);
}
else
{
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getColour(renderOrder[ro]).getRGB());
}
- setting.setDisplay(av.featuresDisplayed
+ setting.setDisplay(av.getFeaturesDisplayed()
.containsKey(renderOrder[ro]));
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(renderOrder[ro]);
if (rorder > -1)
{
}
// Make sure we save none displayed feature settings
- Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours
.keySet().iterator();
while (en.hasNext())
{
Setting setting = new Setting();
setting.setType(key);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getColour(key).getRGB());
setting.setDisplay(false);
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(key);
if (rorder > -1)
{
fs.addSetting(setting);
settingsAdded.addElement(key);
}
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups
.keySet().iterator();
Vector groupsAdded = new Vector();
while (en.hasNext())
}
Group g = new Group();
g.setName(grp);
- g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
+ g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
.getFeatureRenderer().featureGroups.get(grp))
.booleanValue());
fs.addGroup(g);
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
-
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
AnnotationElement ae;
if (aa[i].annotations != null)
{
}
ae.setPosition(a);
- if (aa[i].annotations[a].secondaryStructure != ' '
- && aa[i].annotations[a].secondaryStructure != '\0')
+ if (aa[i].annotations[a].secondaryStructure > ' ')
{
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ "");
}
else
{
- recoverDatasetFor(vamsasSet, al);
+ // recover dataset - passing on flag indicating if this a 'viewless'
+ // sequence set (a.k.a. a stored dataset for the project)
+ recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
+ .getViewportCount() == 0);
}
// ///////////////////////////////
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.rightAlignIds = view.getRightAlignIds();
+ af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(new java.awt.Font(view.getFontName(), view
.getFontStyle(), view.getFontSize()));
af.alignPanel.fontChanged();
// recover featre settings
if (jms.getFeatureSettings() != null)
{
- af.viewport.featuresDisplayed = new Hashtable();
+ af.viewport.setFeaturesDisplayed(new Hashtable());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
gc.setColourByLabel(setting.getColourByLabel());
}
// and put in the feature colour table.
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
setting.getType(), gc);
}
else
{
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
setting.getType(),
new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
{
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
setting.getType(), setting.getOrder());
}
else
{
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
setting.getType(),
fs / jms.getFeatureSettings().getSettingCount());
}
if (setting.getDisplay())
{
- af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+ af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
setting.getColour()));
}
}
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
Hashtable fgtable;
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
}
}
- private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+ boolean ignoreUnrefed)
{
jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
Vector dseqs = null;
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
}
// create a new dataset
if (ds == null)
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
- if (al.getDataset() == null)
+ if (al.getDataset() == null && !ignoreUnrefed)
{
al.setDataset(ds);
}
* vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
{
dsq = sq.getDatasetSequence();
}
-
+ if (sq == null && ignoreUnrefed)
+ {
+ return;
+ }
String sqid = vamsasSeq.getDsseqid();
if (dsq == null)
{
git://source.jalview.org / jalview.git / blobdiff