import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
import java.awt.Color;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
/**
* Collects a set contiguous ranges on a set of sequences
Conservation conserve;
- Vector aaFrequency;
-
boolean displayBoxes = true;
boolean displayText = true;
boolean colourText = false;
/**
+ * True if the group is defined as a group on the alignment, false if it is
+ * just a selection.
+ */
+ boolean isDefined = false;
+
+ /**
* after Olivier's non-conserved only character display
*/
boolean showNonconserved = false;
/**
* group members
*/
- private List<SequenceI> sequences = new ArrayList<SequenceI>();
+ private List<SequenceI> sequences = new ArrayList<>();
/**
* representative sequence for this group (if any)
/**
* Colourscheme applied to group if any
*/
- public ColourSchemeI cs;
+ public ResidueShaderI cs;
// start column (base 0)
int startRes = 0;
public SequenceGroup()
{
groupName = "JGroup:" + this.hashCode();
+ cs = new ResidueShader();
}
/**
ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
boolean colourText, int start, int end)
{
+ this();
this.sequences = sequences;
this.groupName = groupName;
this.displayBoxes = displayBoxes;
this.displayText = displayText;
this.colourText = colourText;
- this.cs = scheme;
+ this.cs = new ResidueShader(scheme);
startRes = start;
endRes = end;
recalcConservation();
*/
public SequenceGroup(SequenceGroup seqsel)
{
+ this();
if (seqsel != null)
{
- sequences = new ArrayList<SequenceI>();
+ sequences = new ArrayList<>();
sequences.addAll(seqsel.sequences);
if (seqsel.groupName != null)
{
}
else
{
- List<SequenceI> allSequences = new ArrayList<SequenceI>();
+ List<SequenceI> allSequences = new ArrayList<>();
for (SequenceI seq : sequences)
{
allSequences.add(seq);
}
/**
- * calculate residue conservation for group - but only if necessary.
+ * calculate residue conservation and colourschemes for group - but only if
+ * necessary. returns true if the calculation resulted in a visible change to
+ * group
+ */
+ public boolean recalcConservation()
+ {
+ return recalcConservation(false);
+ }
+
+ /**
+ * calculate residue conservation for group - but only if necessary. returns
+ * true if the calculation resulted in a visible change to group
+ *
+ * @param defer
+ * when set, colourschemes for this group are not refreshed after
+ * recalculation
*/
- public void recalcConservation()
+ public boolean recalcConservation(boolean defer)
{
if (cs == null && consensus == null && conservation == null)
{
- return;
+ return false;
}
+ // TODO: try harder to detect changes in state in order to minimise
+ // recalculation effort
+ boolean upd = false;
try
{
- Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+ ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
+ upd = true;
}
if (cs != null)
{
cs.setConsensus(cnsns);
+ upd = true;
}
if ((conservation != null)
|| (cs != null && cs.conservationApplied()))
{
- Conservation c = new Conservation(groupName,
- ResidueProperties.propHash, 3, sequences, startRes,
+ Conservation c = new Conservation(groupName, sequences, startRes,
endRes + 1);
c.calculate();
c.verdict(false, consPercGaps);
cs.setConservation(c);
}
}
+ // eager update - will cause a refresh of overview regardless
+ upd = true;
}
- if (cs != null)
+ if (cs != null && !defer)
{
+ // TODO: JAL-2034 should cs.alignmentChanged modify return state
cs.alignmentChanged(context != null ? context : this, null);
+ return true;
+ }
+ else
+ {
+ return upd;
}
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
System.out.println("Out of memory loading groups: " + err);
}
-
+ return upd;
}
private void _updateConservationRow(Conservation c)
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
- public Hashtable[] consensusData = null;
+ public ProfilesI consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
+ private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
{
/**
* @return the representative sequence for this group
*/
+ @Override
public SequenceI getSeqrep()
{
return seqrep;
* @param seqrep
* the seqrep to set (null means no sequence representative)
*/
+ @Override
public void setSeqrep(SequenceI seqrep)
{
this.seqrep = seqrep;
*
* @return true if group has a sequence representative
*/
+ @Override
public boolean hasSeqrep()
{
return seqrep != null;
{
SequenceGroup sgroup = new SequenceGroup(this);
SequenceI[] insect = getSequencesInOrder(alignment);
- sgroup.sequences = new ArrayList<SequenceI>();
+ sgroup.sequences = new ArrayList<>();
for (int s = 0; insect != null && s < insect.length; s++)
{
if (map == null || map.containsKey(insect[s]))
/**
*
- * @return automatically calculated consensus row
+ * @return automatically calculated consensus row note: the row is a stub if a
+ * consensus calculation has not yet been performed on the group
*/
public AlignmentAnnotation getConsensus()
{
{
// TODO add in other methods like 'getAlignmentAnnotation(String label),
// etc'
- ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+ ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
synchronized (sequences)
{
for (SequenceI seq : sequences)
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> aa = new ArrayList<>();
+ if (calcId == null)
+ {
+ return aa;
+ }
for (AlignmentAnnotation a : getAlignmentAnnotation())
{
- if (a.getCalcId() == calcId)
+ if (calcId.equals(a.getCalcId()))
{
aa.add(a);
}
return aa;
}
- /**
- * Returns a list of annotations that match the specified sequenceRef, calcId
- * and label, ignoring null values.
- *
- * @return list of AlignmentAnnotation objects
- */
@Override
public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : getAlignmentAnnotation())
{
- if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
- && ann.sequenceRef != null && ann.sequenceRef == seq
- && ann.label != null && ann.label.equals(label))
+ if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
+ .equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
+ && (label == null || (ann.label != null && ann.label
+ .equals(label))))
{
aa.add(ann);
}
private AnnotatedCollectionI context;
/**
- * set the alignment or group context for this group
+ * Sets the alignment or group context for this group, and whether it is
+ * defined as a group
*
- * @param context
+ * @param ctx
+ * the context for the group
+ * @param defined
+ * whether the group is defined on the alignment or is just a
+ * selection
+ * @throws IllegalArgumentException
+ * if setting the context would result in a circular reference chain
*/
- public void setContext(AnnotatedCollectionI context)
+ public void setContext(AnnotatedCollectionI ctx, boolean defined)
{
- this.context = context;
+ setContext(ctx);
+ this.isDefined = defined;
+ }
+
+ /**
+ * Sets the alignment or group context for this group
+ *
+ * @param ctx
+ * the context for the group
+ * @throws IllegalArgumentException
+ * if setting the context would result in a circular reference chain
+ */
+ public void setContext(AnnotatedCollectionI ctx)
+ {
+ AnnotatedCollectionI ref = ctx;
+ while (ref != null)
+ {
+ if (ref == this || ref.getContext() == ctx)
+ {
+ throw new IllegalArgumentException(
+ "Circular reference in SequenceGroup.context");
+ }
+ ref = ref.getContext();
+ }
+ this.context = ctx;
}
/*
{
return context;
}
+
+ public boolean isDefined()
+ {
+ return isDefined;
+ }
+
+ public void setColourScheme(ColourSchemeI scheme)
+ {
+ if (cs == null)
+ {
+ cs = new ResidueShader();
+ }
+ cs.setColourScheme(scheme);
+ }
+
+ public void setGroupColourScheme(ResidueShaderI scheme)
+ {
+ cs = scheme;
+ }
+
+ public ColourSchemeI getColourScheme()
+ {
+ return cs == null ? null : cs.getColourScheme();
+ }
+
+ public ResidueShaderI getGroupColourScheme()
+ {
+ return cs;
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ if (context != null) {
+ return context.isNucleotide();
+ }
+ return false;
+ }
+
+ /**
+ * @param seq
+ * @return true if seq is a member of the group
+ */
+
+ public boolean contains(SequenceI seq1)
+ {
+ return sequences.contains(seq1);
+ }
+
+ /**
+ * @param seq
+ * @param apos
+ * @return true if startRes<=apos and endRes>=apos and seq is in the group
+ */
+ public boolean contains(SequenceI seq, int apos)
+ {
+ return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+ }
}
git://source.jalview.org / jalview.git / blobdiff