*/
package jalview.datamodel;
-import jalview.analysis.AAFrequency;
-import jalview.analysis.Conservation;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.Arrays;
+import java.util.Collection;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.ColourSchemeI;
/**
* Collects a set contiguous ranges on a set of sequences
*/
public class SequenceGroup implements AnnotatedCollectionI
{
+ // TODO ideally this event notification functionality should be separated into
+ // a
+ // subclass of ViewportProperties similarly to ViewportRanges. Done here as
+ // quick fix for JAL-2665
+ public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+ // end of event notification functionality initialisation
+
String groupName;
String description;
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;
/**
* 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;
+ /**
+ * start column (base 0)
+ */
+ private int startRes = 0;
- // end column (base 0)
- int endRes = 0;
+ /**
+ * end column (base 0)
+ */
+ private int endRes = 0;
public Color outlineColour = Color.black;
*/
private boolean normaliseSequenceLogo;
- /**
- * @return the includeAllConsSymbols
+ /*
+ * visibility of rows or represented rows covered by group
*/
- public boolean isShowSequenceLogo()
- {
- return showSequenceLogo;
- }
+ private boolean hidereps = false;
+
+ /*
+ * visibility of columns intersecting this group
+ */
+ private boolean hidecols = false;
+
+ AlignmentAnnotation consensus = null;
+
+ AlignmentAnnotation conservation = null;
+
+ private boolean showConsensusHistogram;
+
+ private AnnotatedCollectionI context;
/**
* Creates a new SequenceGroup object.
public SequenceGroup()
{
groupName = "JGroup:" + this.hashCode();
+ cs = new ResidueShader();
+ sequences = new ArrayList<>();
}
/**
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)
{
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
+
startRes = seqsel.startRes;
endRes = seqsel.endRes;
- cs = seqsel.cs;
+ cs = new ResidueShader((ResidueShader) seqsel.cs);
if (seqsel.description != null)
{
description = new String(seqsel.description);
}
hidecols = seqsel.hidecols;
hidereps = seqsel.hidereps;
+ showNonconserved = seqsel.showNonconserved;
+ showSequenceLogo = seqsel.showSequenceLogo;
+ normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
+ showConsensusHistogram = seqsel.showConsensusHistogram;
idColour = seqsel.idColour;
outlineColour = seqsel.outlineColour;
seqrep = seqsel.seqrep;
}
}
+ /**
+ * Constructor that copies the given list of sequences
+ *
+ * @param seqs
+ */
+ public SequenceGroup(List<SequenceI> seqs)
+ {
+ this();
+ this.sequences.addAll(seqs);
+ }
+
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
{
int iSize = sequences.size();
for (int i = 0, ipos = 0; i < inorder.length; i++)
{
SequenceI seq = inorder[i];
-
- seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
- if (seqs[ipos] != null)
+ SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes,
+ endRes + 1);
+ if (seqipos != null)
{
- seqs[ipos].setDescription(seq.getDescription());
- seqs[ipos].setDBRef(seq.getDBRef());
- seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
- if (seq.getDatasetSequence() != null)
- {
- seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
- }
-
if (seq.getAnnotation() != null)
{
AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
if (alann != null)
{
boolean found = false;
- for (int pos = 0; pos < alann.length; pos++)
+ for (int pos = 0, np = alann.length; pos < np; pos++)
{
if (alann[pos] == tocopy)
{
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
- seqs[ipos].addAlignmentAnnotation(newannot);
+ ContactMatrixI cm = seq
+ .getContactMatrixFor(seq.getAnnotation()[a]);
+ if (cm != null)
+ {
+ seqs[ipos].addContactListFor(newannot, cm);
+ }
+ seqipos.addAlignmentAnnotation(newannot);
}
}
ipos++;
}
else
{
- List<SequenceI> allSequences = new ArrayList<SequenceI>();
+ List<SequenceI> allSequences = new ArrayList<>();
for (SequenceI seq : sequences)
{
allSequences.add(seq);
if (s != null && !sequences.contains(s))
{
sequences.add(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() - 1, sequences.size());
}
if (recalc)
}
/**
- * 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 void recalcConservation()
+ 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 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);
+ jalview.bin.Console
+ .outPrintln("Out of memory loading groups: " + err);
}
-
+ return upd;
}
private void _updateConservationRow(Conservation c)
conservation.description = "Conservation for group " + getName()
+ " less than " + consPercGaps + "% gaps";
// preserve width if already set
- int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
- : endRes + 1)
+ int aWidth = (conservation.annotations != null)
+ ? (endRes < conservation.annotations.length
+ ? conservation.annotations.length
+ : endRes + 1)
: endRes + 1;
conservation.annotations = null;
conservation.annotations = new Annotation[aWidth]; // should be alignment
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)
{
consensus.description = "Percent Identity";
consensusData = cnsns;
// preserve width if already set
- int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
- : endRes + 1)
+ int aWidth = (consensus.annotations != null)
+ ? (endRes < consensus.annotations.length
+ ? consensus.annotations.length
+ : endRes + 1)
: endRes + 1;
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth]; // should be alignment width
synchronized (sequences)
{
sequences.remove(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() + 1, sequences.size());
if (recalc)
{
/**
* Set the first column selected by this group. Runs from 0<=i<N_cols
*
- * @param i
+ * @param newStart
*/
- public void setStartRes(int i)
+ public void setStartRes(int newStart)
{
- startRes = i;
+ int before = startRes;
+ startRes = Math.max(0, newStart); // sanity check for negative start column
+ // positions
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+
}
/**
*/
public void setEndRes(int i)
{
+ int before = endRes;
endRes = i;
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
}
/**
/**
* @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;
}
/**
- * visibility of rows or represented rows covered by group
- */
- private boolean hidereps = false;
-
- /**
* set visibility of sequences covered by (if no sequence representative is
* defined) or represented by this group.
*
}
/**
- * visibility of columns intersecting this group
- */
- private boolean hidecols = false;
-
- /**
* set intended visibility of columns covered by this group
*
* @param visibility
{
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]))
this.showNonconserved = displayNonconserved;
}
- AlignmentAnnotation consensus = null, conservation = null;
-
- /**
- * flag indicating if consensus histogram should be rendered
- */
- private boolean showConsensusHistogram;
-
/**
* set this alignmentAnnotation object as the one used to render consensus
* annotation
/**
*
- * @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()
{
{
if (consensus.annotations[i] != null)
{
- if (consensus.annotations[i].description.charAt(0) == '[')
+ String desc = consensus.annotations[i].description;
+ if (desc.length() > 1 && desc.charAt(0) == '[')
{
- seqs.append(consensus.annotations[i].description.charAt(1));
+ seqs.append(desc.charAt(1));
}
else
{
{
// 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>();
- for (AlignmentAnnotation a : getAlignmentAnnotation())
- {
- if (a.getCalcId() == calcId)
- {
- aa.add(a);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
}
- /**
- * 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>();
- 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))
- {
- aa.add(ann);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
}
/**
*/
public boolean hasAnnotation(String calcId)
{
- if (calcId != null && !"".equals(calcId))
- {
- for (AlignmentAnnotation a : getAlignmentAnnotation())
- {
- if (a.getCalcId() == calcId)
- {
- return true;
- }
- }
- }
- return false;
+ return AlignmentAnnotation
+ .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
}
/**
{
synchronized (sequences)
{
+ int before = sequences.size();
sequences.clear();
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+ sequences.size());
}
}
- private AnnotatedCollectionI context;
+ /**
+ * Sets the alignment or group context for this group, and whether it is
+ * defined as a group
+ *
+ * @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 ctx, boolean defined)
+ {
+ setContext(ctx);
+ this.isDefined = defined;
+ }
/**
- * set the alignment or group context for this group
+ * Sets the alignment or group context for this group
*
- * @param context
+ * @param ctx
+ * the context for the group
+ * @throws IllegalArgumentException
+ * if setting the context would result in a circular reference chain
*/
- public void setContext(AnnotatedCollectionI context)
+ public void setContext(AnnotatedCollectionI ctx)
{
- this.context = context;
+ 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);
+ }
+
+ ////
+ //// Contact Matrix Holder Boilerplate
+ ////
+ ContactMapHolder cmholder = new ContactMapHolder();
+
+ @Override
+ public Collection<ContactMatrixI> getContactMaps()
+ {
+ return cmholder.getContactMaps();
+ }
+
+ @Override
+ public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+ {
+ return cmholder.getContactMatrixFor(ann);
+ }
+
+ @Override
+ public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+ {
+ return cmholder.getContactListFor(_aa, column);
+ }
+
+ @Override
+ public AlignmentAnnotation addContactList(ContactMatrixI cm)
+ {
+ AlignmentAnnotation aa = cmholder.addContactList(cm);
+
+ Annotation _aa[] = new Annotation[getWidth()];
+ Annotation dummy = new Annotation(0.0f);
+ for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+ {
+ ;
+ }
+ aa.annotations = _aa;
+ // TODO passing annotations back to context to be added
+ return aa;
+ }
+
+ @Override
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm)
+ {
+ cmholder.addContactListFor(annotation, cm);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff