*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
object.setVersion(jalview.bin.Cache.getDefault("VERSION",
"Development Build"));
- jalview.datamodel.AlignmentI jal = av.getAlignment();
+ /**
+ * rjal is full height alignment, jal is actual alignment with full metadata
+ * but excludes hidden sequences.
+ */
+ jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
if (av.hasHiddenRows())
{
- jal = jal.getHiddenSequences().getFullAlignment();
+ rjal = jal.getHiddenSequences().getFullAlignment();
}
SequenceSet vamsasSet = new SequenceSet();
{
// switch jal and the dataset
jal = jal.getDataset();
+ rjal = jal;
}
}
if (jal.getProperties() != null)
Set<String> calcIdSet = new HashSet<String>();
// SAVE SEQUENCES
- for (int i = 0; i < jal.getHeight(); i++)
+ for (int i = 0; i < rjal.getHeight(); i++)
{
- final SequenceI jds = jal.getSequenceAt(i);
+ final SequenceI jds = rjal.getSequenceAt(i);
final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
: jds.getDatasetSequence();
String id = seqHash(jds);
// Store any sequences this sequence represents
if (av.hasHiddenRows())
{
+ // use rjal, contains the full height alignment
jseq.setHidden(av.getAlignment().getHiddenSequences()
.isHidden(jds));
- if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+ if (av.isHiddenRepSequence(rjal.getSequenceAt(i)))
{
jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jal.getSequenceAt(i))
- .getSequencesInOrder(jal);
+ .getRepresentedSequences(rjal.getSequenceAt(i))
+ .getSequencesInOrder(rjal);
for (int h = 0; h < reps.length; h++)
{
- if (reps[h] != jal.getSequenceAt(i))
+ if (reps[h] != rjal.getSequenceAt(i))
{
- jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ jseq.addHiddenSequences(rjal.findIndex(reps[h]));
}
}
}
}
+ // mark sequence as reference - if it is the reference for this view
+ if (jal.hasSeqrep())
+ {
+ jseq.setViewreference(rjal.getSequenceAt(i) == jal.getSeqrep());
+ }
}
+ // TODO: omit sequence features from each alignment view's XML dump if we
+ // are storing dataset
if (jds.getSequenceFeatures() != null)
{
jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
alc.addAlcodMap(alcmap);
}
}
-
+ // TODO: delete this ? dead code from 2.8.3->2.9 ?
// {
// AlcodonFrame alc = new AlcodonFrame();
// vamsasSet.addAlcodonFrame(alc);
.toArray(new String[0]);
Vector<String> settingsAdded = new Vector<String>();
- Object gstyle = null;
- GraduatedColor gcol = null;
if (renderOrder != null)
{
for (String featureType : renderOrder)
{
- gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ FeatureColourI fcol = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer()
.getFeatureStyle(featureType);
Setting setting = new Setting();
setting.setType(featureType);
- if (gstyle instanceof GraduatedColor)
+ if (!fcol.isSimpleColour())
{
- gcol = (GraduatedColor) gstyle;
- setting.setColour(gcol.getMaxColor().getRGB());
- setting.setMincolour(gcol.getMinColor().getRGB());
- setting.setMin(gcol.getMin());
- setting.setMax(gcol.getMax());
- setting.setColourByLabel(gcol.isColourByLabel());
- setting.setAutoScale(gcol.isAutoScale());
- setting.setThreshold(gcol.getThresh());
- setting.setThreshstate(gcol.getThreshType());
+ setting.setColour(fcol.getMaxColour().getRGB());
+ setting.setMincolour(fcol.getMinColour().getRGB());
+ setting.setMin(fcol.getMin());
+ setting.setMax(fcol.getMax());
+ setting.setColourByLabel(fcol.isColourByLabel());
+ setting.setAutoScale(fcol.isAutoScaled());
+ setting.setThreshold(fcol.getThreshold());
+ // -1 = No threshold, 0 = Below, 1 = Above
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1
+ : (fcol.isBelowThreshold() ? 0 : -1));
}
else
{
- setting.setColour(((Color) gstyle).getRGB());
+ setting.setColour(fcol.getColour().getRGB());
}
setting.setDisplay(av.getFeaturesDisplayed().isVisible(
groupsAdded.addElement(grp);
}
jms.setFeatureSettings(fs);
-
}
if (av.hasHiddenColumns())
List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
boolean multipleView = false;
-
+ SequenceI referenceseqForView = null;
JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
int vi = 0; // counter in vamsasSeq array
for (int i = 0; i < jseqs.length; i++)
vi++;
}
+ if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
+ {
+ referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
+ }
+
if (jseqs[i].getHidden())
{
if (hiddenSeqs == null)
hiddenSeqs.add(seqRefIds.get(seqId));
}
-
}
// /
AlignmentI al = new Alignment(orderedSeqs);
+ if (referenceseqForView != null)
+ {
+ al.setSeqrep(referenceseqForView);
+ }
// / Add the alignment properties
for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
{
.getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
+ if (al.hasSeqrep())
+ {
+ af.getViewport().setColourByReferenceSeq(true);
+ af.getViewport().setDisplayReferenceSeq(true);
+ }
+
af.viewport.setGatherViewsHere(view.getGatheredViews());
if (view.getSequenceSetId() != null)
af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
- Hashtable featureGroups = new Hashtable();
- Hashtable featureColours = new Hashtable();
- Hashtable featureOrder = new Hashtable();
+ Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
+ Map<String, Float> featureOrder = new Hashtable<String, Float>();
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
if (setting.hasMincolour())
{
- GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
- new java.awt.Color(setting.getMincolour()),
- new java.awt.Color(setting.getColour()),
- setting.getMin(), setting.getMax()) : new GraduatedColor(
- new java.awt.Color(setting.getMincolour()),
- new java.awt.Color(setting.getColour()), 0, 1);
+ FeatureColourI gc = setting.hasMin() ? new FeatureColour(
+ new Color(setting.getMincolour()), new Color(
+ setting.getColour()), setting.getMin(),
+ setting.getMax()) : new FeatureColour(new Color(
+ setting.getMincolour()), new Color(setting.getColour()),
+ 0, 1);
if (setting.hasThreshold())
{
- gc.setThresh(setting.getThreshold());
- gc.setThreshType(setting.getThreshstate());
+ gc.setThreshold(setting.getThreshold());
+ int threshstate = setting.getThreshstate();
+ // -1 = None, 0 = Below, 1 = Above threshold
+ if (threshstate == 0)
+ {
+ gc.setBelowThreshold(true);
+ }
+ else if (threshstate == 1)
+ {
+ gc.setAboveThreshold(true);
+ }
}
gc.setAutoScaled(true); // default
if (setting.hasAutoScale())
}
else
{
- featureColours.put(setting.getType(),
- new java.awt.Color(setting.getColour()));
+ featureColours.put(setting.getType(), new FeatureColour(
+ new Color(setting.getColour())));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
fdi.setVisible(setting.getType());
}
}
- Hashtable fgtable = new Hashtable();
+ Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
git://source.jalview.org / jalview.git / blobdiff