// a subclass of ViewportProperties similarly to ViewportRanges.
// Done here as a 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);
+ }
- private String groupName;
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+ // end of event notification functionality initialisation
- private String description;
+ String groupName;
- private AnnotatedCollectionI context;
+ String description;
+
+ Conservation conserve;
- private Conservation conservationData;
+ Conservation conservationData;
- private ProfilesI consensusProfiles;
+ ProfilesI consensusProfiles;
- private ProfilesI hmmProfiles;
+ ProfilesI hmmProfiles;
- private boolean displayBoxes = true;
+ boolean displayBoxes = true;
- private boolean displayText = true;
+ boolean displayText = true;
- private boolean colourText = false;
+ boolean colourText = false;
/*
* true if the group is defined as a group on the alignment, false if it is
* just a selection
*/
- private boolean isDefined;
+ boolean isDefined = false;
/*
* after Olivier's non-conserved only character display
*/
- private boolean showNonconserved;
+ boolean showNonconserved = false;
/*
* sequences in the group
*/
- private List<SequenceI> sequences = new ArrayList<>();
+ private List<SequenceI> sequences;
/*
* representative sequence for this group (if any)
*/
- private SequenceI seqrep;
+ private SequenceI seqrep = null;
- /*
- * HMM consensus sequence for group (if any)
- */
- private SequenceI hmmConsensus;
-
- private int width = -1;
+ int width = -1;
/*
* colour scheme applied to group if any
*/
public ResidueShaderI cs;
- // start column (base 0)
- private int startRes;
+ /**
+ * start column (base 0)
+ */
+ private int startRes = 0;
- // end column (base 0)
- private int endRes;
+ /**
+ * end column (base 0)
+ */
+ private int endRes = 0;
public Color outlineColour = Color.black;
- public Color idColour;
+ public Color idColour = null;
- public int thresholdTextColour;
+ public int thresholdTextColour = 0;
public Color textColour = Color.black;
*/
private boolean ignoreGapsInConsensus = true;
- private boolean showSequenceLogo;
+ private boolean showSequenceLogo = false;
private boolean normaliseSequenceLogo;
- private boolean showConsensusHistogram;
-
/*
* properties for HMM information annotation
*/
private boolean hmmUseInfoLetterHeight;
- private boolean showHMMSequenceLogo;
+ private boolean hmmShowSequenceLogo;
private boolean hmmNormaliseSequenceLogo;
/*
* visibility of rows or represented rows covered by group
*/
- private boolean hidereps;
+ private boolean hidereps = false;
/*
* visibility of columns intersecting this group
*/
private boolean hidecols;
- private AlignmentAnnotation consensus;
+ AlignmentAnnotation consensus = null;
- private AlignmentAnnotation conservation;
+ AlignmentAnnotation conservation = null;
private AlignmentAnnotation hmmInformation;
+
+ private boolean showConsensusHistogram;
+
+ private AnnotatedCollectionI context;
+
/**
* Constructor, assigning a generated default name of "JGroup:" with object
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
+ sequences = new ArrayList<>();
}
/**
* copy constructor
*
* @param seqsel
+ * @param keepsequences
+ * if false do not add sequences from seqsel to new instance
*/
public SequenceGroup(SequenceGroup seqsel)
{
this();
+
if (seqsel != null)
{
sequences = new ArrayList<>();
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
+
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
showSequenceLogo = seqsel.showSequenceLogo;
normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
showConsensusHistogram = seqsel.showConsensusHistogram;
- showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+ hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
hmmShowHistogram = seqsel.hmmShowHistogram;
idColour = seqsel.idColour;
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
- if (seqsel.conservationData != null)
+ if (seqsel.conserve != null)
{
+ // todo avoid doing this if we don't actually want derived calculations
+ // !
recalcConservation(); // safer than
// aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
}
}
}
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
-
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- public void removePropertyChangeListener(PropertyChangeListener listener)
+ /**
+ * Constructor that copies the given list of sequences
+ *
+ * @param seqs
+ */
+ public SequenceGroup(List<SequenceI> seqs)
{
- changeSupport.removePropertyChangeListener(listener);
+ this();
+ this.sequences.addAll(seqs);
}
public boolean isShowSequenceLogo()
seqs[ipos].setDescription(seq.getDescription());
seqs[ipos].setDBRefs(seq.getDBRefs());
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
- seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
if (seq.getDatasetSequence() != null)
{
seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
*/
public Conservation getConservation()
{
- return conservationData;
+ return conserve;
}
/**
*/
public void setConservation(Conservation c)
{
- conservationData = c;
+ conserve = c;
}
/**
*/
public boolean recalcConservation()
{
- return recalcAnnotations(false);
+ return recalcConservation(false);
}
/**
* when set, colourschemes for this group are not refreshed after
* recalculation
*/
- public boolean recalcAnnotations(boolean defer)
+ public boolean recalcConservation(boolean defer)
{
if (cs == null && consensus == null && conservation == null
&& hmmInformation == null)
ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
(endRes + 1) - startRes, startRes, endRes + 1,
- showHMMSequenceLogo, hmmIgnoreBelowBackground,
- hmmUseInfoLetterHeight);
- _updateInformationRow(info, sequences.size());
+ hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
+ _updateInformationRow(info);
upd = true;
}
if (consensus != null)
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
+ public ProfilesI consensusData = null;
+
private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
}
consensus.label = "Consensus for " + getName();
consensus.description = "Percent Identity";
- consensusProfiles = cnsns;
+ consensusData = cnsns;
// preserve width if already set
int aWidth = (consensus.annotations != null)
? (endRes < consensus.annotations.length
}
/**
- * Recalculates the information content on the HMM annotation.
+ * Recalculates the information content on the HMM annotation
*
* @param cnsns
- * @param nseq
*/
- private void _updateInformationRow(ProfilesI cnsns, long nseq)
+ private void _updateInformationRow(ProfilesI cnsns)
{
if (hmmInformation == null)
{
// width
hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
- endRes + 1, nseq, 0f);
+ endRes + 1);
}
/**
/**
* 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)
{
int before = startRes;
- startRes = i;
- changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+ startRes= Math.max(0,newStart); // sanity check for negative start column positions
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+
+
+
}
/**
ignoreGapsInConsensus = state;
}
- public boolean isIgnoreGapsConsensus()
+ public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensus;
}
// recalcConservation(); TODO don't know what to do here next
}
this.hmmShowHistogram = state;
-
}
public boolean isShowHMMSequenceLogo()
{
- return showHMMSequenceLogo;
+ return hmmShowSequenceLogo;
}
- public void setshowHMMSequenceLogo(boolean state)
+ public void setShowHMMSequenceLogo(boolean state)
{
- showHMMSequenceLogo = state;
-
+ hmmShowSequenceLogo = state;
}
public boolean isNormaliseHMMSequenceLogo()
public void setNormaliseHMMSequenceLogo(boolean state)
{
- normaliseSequenceLogo = state;
- }
-
- @Override
- public SequenceI getHmmConsensus()
- {
- return hmmConsensus;
- }
-
- @Override
- public void setHmmConsensus(SequenceI hmmSeq)
- {
- this.hmmConsensus = hmmSeq;
+ hmmNormaliseSequenceLogo = state;
}
public ProfilesI getConsensusData()
this.hmmProfiles = hmmProfiles;
}
+ @Override
+ public List<SequenceI> getHmmSequences()
+ {
+ List<SequenceI> result = new ArrayList<>();
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ SequenceI seq = sequences.get(i);
+ if (seq.hasHMMProfile())
+ {
+ result.add(seq);
+ }
+ }
+ return result;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff