/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.Arrays;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
/**
* 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 Vector<SequenceI> sequences = new Vector<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;
+ // end column (base 0)
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();
}
/**
* @param end
* last column of group
*/
- public SequenceGroup(Vector sequences, String groupName,
+ public SequenceGroup(List<SequenceI> sequences, String groupName,
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 Vector();
- Enumeration<SequenceI> sq = seqsel.sequences.elements();
- while (sq.hasMoreElements())
- {
- sequences.addElement(sq.nextElement());
- }
- ;
+ sequences = new ArrayList<>();
+ sequences.addAll(seqsel.sequences);
if (seqsel.groupName != null)
{
groupName = new String(seqsel.groupName);
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;
}
}
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
{
int iSize = sequences.size();
if (seqs[ipos] != null)
{
seqs[ipos].setDescription(seq.getDescription());
- seqs[ipos].setDBRef(seq.getDBRef());
+ seqs[ipos].setDBRefs(seq.getDBRefs());
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
}
}
if (!found)
+ {
continue;
+ }
}
AlignmentAnnotation newannot = new AlignmentAnnotation(
seq.getAnnotation()[a]);
{
if (hiddenReps == null)
{
+ // TODO: need a synchronizedCollection here ?
return sequences;
}
else
{
- Vector allSequences = new Vector();
- SequenceI seq;
- for (int i = 0; i < sequences.size(); i++)
+ List<SequenceI> allSequences = new ArrayList<>();
+ for (SequenceI seq : sequences)
{
- seq = sequences.elementAt(i);
- allSequences.addElement(seq);
+ allSequences.add(seq);
if (hiddenReps.containsKey(seq))
{
SequenceCollectionI hsg = hiddenReps.get(seq);
{
if (seq2 != seq && !allSequences.contains(seq2))
{
- allSequences.addElement(seq2);
+ allSequences.add(seq2);
}
}
}
*/
public void addSequence(SequenceI s, boolean recalc)
{
- if (s != null && !sequences.contains(s))
+ synchronized (sequences)
{
- sequences.addElement(s);
- }
+ if (s != null && !sequences.contains(s))
+ {
+ sequences.add(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() - 1, sequences.size());
+ }
- if (recalc)
- {
- recalcConservation();
+ if (recalc)
+ {
+ recalcConservation();
+ }
}
}
}
/**
- * 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)
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
*/
public void addOrRemove(SequenceI s, boolean recalc)
{
- if (sequences.contains(s))
- {
- deleteSequence(s, recalc);
- }
- else
+ synchronized (sequences)
{
- addSequence(s, recalc);
+ if (sequences.contains(s))
+ {
+ deleteSequence(s, recalc);
+ }
+ else
+ {
+ addSequence(s, recalc);
+ }
}
}
/**
- * DOCUMENT ME!
+ * remove
*
* @param s
- * DOCUMENT ME!
+ * to be removed
* @param recalc
- * DOCUMENT ME!
+ * true means recalculate conservation
*/
public void deleteSequence(SequenceI s, boolean recalc)
{
- sequences.removeElement(s);
-
- if (recalc)
+ synchronized (sequences)
{
- recalcConservation();
+ sequences.remove(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() + 1, sequences.size());
+
+ if (recalc)
+ {
+ recalcConservation();
+ }
}
}
*/
public void setStartRes(int i)
{
+ int before = startRes;
startRes = i;
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
}
/**
*/
public void setEndRes(int i)
{
+ int before = endRes;
endRes = i;
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return number of sequences in group
*/
public int getSize()
{
}
/**
- * DOCUMENT ME!
- *
* @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return the ith sequence
*/
public SequenceI getSequenceAt(int i)
{
- return sequences.elementAt(i);
+ return sequences.get(i);
}
/**
- * DOCUMENT ME!
- *
* @param state
- * DOCUMENT ME!
+ * colourText
*/
public void setColourText(boolean state)
{
}
/**
- * DOCUMENT ME!
+ * computes the width of current set of sequences and returns it
*
* @return DOCUMENT ME!
*/
@Override
public int getWidth()
{
- // MC This needs to get reset when characters are inserted and deleted
- if (sequences.size() > 0)
- {
- width = sequences.elementAt(0).getLength();
- }
-
- for (int i = 1; i < sequences.size(); i++)
+ synchronized (sequences)
{
- SequenceI seq = sequences.elementAt(i);
-
- if (seq.getLength() > width)
+ // MC This needs to get reset when characters are inserted and deleted
+ boolean first = true;
+ for (SequenceI seq : sequences)
{
- width = seq.getLength();
+ if (first || seq.getLength() > width)
+ {
+ width = seq.getLength();
+ first = false;
+ }
}
+ return width;
}
-
- return width;
}
/**
*/
public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
{
- int sSize = sequences.size();
- int alHeight = al.getHeight();
+ synchronized (sequences)
+ {
+ int sSize = sequences.size();
+ int alHeight = al.getHeight();
- SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
+ SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
- int index = 0;
- for (int i = 0; i < alHeight && index < sSize; i++)
- {
- if (sequences.contains(al.getSequenceAt(i)))
+ int index = 0;
+ for (int i = 0; i < alHeight && index < sSize; i++)
{
- seqs[(trim) ? index : i] = al.getSequenceAt(i);
- index++;
+ if (sequences.contains(al.getSequenceAt(i)))
+ {
+ seqs[(trim) ? index : i] = al.getSequenceAt(i);
+ index++;
+ }
}
- }
- if (index == 0)
- {
- return null;
- }
- if (!trim)
- {
- return seqs;
- }
- if (index < seqs.length)
- {
- SequenceI[] dummy = seqs;
- seqs = new SequenceI[index];
- while (--index >= 0)
+ if (index == 0)
+ {
+ return null;
+ }
+ if (!trim)
{
- seqs[index] = dummy[index];
- dummy[index] = null;
+ return seqs;
+ }
+ if (index < seqs.length)
+ {
+ SequenceI[] dummy = seqs;
+ seqs = new SequenceI[index];
+ while (--index >= 0)
+ {
+ seqs[index] = dummy[index];
+ dummy[index] = null;
+ }
}
+ return seqs;
}
- return seqs;
}
/**
/**
* @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 Vector();
+ sgroup.sequences = new ArrayList<>();
for (int s = 0; insect != null && s < insect.length; s++)
{
if (map == null || map.containsKey(insect[s]))
{
- sgroup.sequences.addElement(insect[s]);
+ sgroup.sequences.add(insect[s]);
}
}
- // Enumeration en =getSequences(hashtable).elements();
- // while (en.hasMoreElements())
- // {
- // SequenceI elem = (SequenceI) en.nextElement();
- // if (alignment.getSequences().contains(elem))
- // {
- // sgroup.addSequence(elem, false);
- // }
- // }
return sgroup;
}
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()
{
{
// TODO add in other methods like 'getAlignmentAnnotation(String label),
// etc'
- ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
- for (SequenceI seq : sequences)
+ ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
+ synchronized (sequences)
{
- AlignmentAnnotation[] aa = seq.getAnnotation();
- if (aa != null)
+ for (SequenceI seq : sequences)
{
- for (AlignmentAnnotation al : aa)
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
{
- if (al.groupRef == this)
+ for (AlignmentAnnotation al : aa)
{
- annot.add(al);
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
}
}
}
- }
- if (consensus != null)
- {
- annot.add(consensus);
- }
- if (conservation != null)
- {
- annot.add(conservation);
+ if (consensus != null)
+ {
+ annot.add(consensus);
+ }
+ if (conservation != null)
+ {
+ annot.add(conservation);
+ }
}
return annot.toArray(new AlignmentAnnotation[0]);
}
@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);
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ 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);
}
+ /**
+ * Remove all sequences from the group (leaving other properties unchanged).
+ */
public void clear()
{
- sequences.clear();
+ 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff