X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=0431708b7344400a3e7433313ae6f71cbd36e5e7;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=b7ec9f95da131f0803a0ff70acf4238d36ea1216;hpb=4306800413a28da102c15fe7301bcac7816445fe;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index b7ec9f9..0431708 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -48,69 +48,82 @@ public class SequenceGroup implements AnnotatedCollectionI // 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 sequences = new ArrayList<>(); + private List 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; @@ -121,12 +134,10 @@ public class SequenceGroup implements AnnotatedCollectionI */ private boolean ignoreGapsInConsensus = true; - private boolean showSequenceLogo; + private boolean showSequenceLogo = false; private boolean normaliseSequenceLogo; - private boolean showConsensusHistogram; - /* * properties for HMM information annotation */ @@ -134,7 +145,7 @@ public class SequenceGroup implements AnnotatedCollectionI private boolean hmmUseInfoLetterHeight; - private boolean showHMMSequenceLogo; + private boolean hmmShowSequenceLogo; private boolean hmmNormaliseSequenceLogo; @@ -143,18 +154,23 @@ public class SequenceGroup implements AnnotatedCollectionI /* * 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 @@ -164,6 +180,7 @@ public class SequenceGroup implements AnnotatedCollectionI { groupName = "JGroup:" + this.hashCode(); cs = new ResidueShader(); + sequences = new ArrayList<>(); } /** @@ -200,10 +217,13 @@ public class SequenceGroup implements AnnotatedCollectionI * 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<>(); @@ -215,6 +235,7 @@ public class SequenceGroup implements AnnotatedCollectionI displayBoxes = seqsel.displayBoxes; displayText = seqsel.displayText; colourText = seqsel.colourText; + startRes = seqsel.startRes; endRes = seqsel.endRes; cs = new ResidueShader((ResidueShader) seqsel.cs); @@ -228,7 +249,7 @@ public class SequenceGroup implements AnnotatedCollectionI showSequenceLogo = seqsel.showSequenceLogo; normaliseSequenceLogo = seqsel.normaliseSequenceLogo; showConsensusHistogram = seqsel.showConsensusHistogram; - showHMMSequenceLogo = seqsel.showHMMSequenceLogo; + hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo; hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo; hmmShowHistogram = seqsel.hmmShowHistogram; idColour = seqsel.idColour; @@ -241,25 +262,25 @@ public class SequenceGroup implements AnnotatedCollectionI 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 seqs) { - changeSupport.removePropertyChangeListener(listener); + this(); + this.sequences.addAll(seqs); } public boolean isShowSequenceLogo() @@ -276,17 +297,15 @@ public class SequenceGroup implements AnnotatedCollectionI 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].setDBRefs(seq.getDBRefs()); - seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures()); - seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence()); + seqipos.setDescription(seq.getDescription()); + seqipos.setDBRefs(seq.getDBRefs()); + seqipos.setSequenceFeatures(seq.getSequenceFeatures()); if (seq.getDatasetSequence() != null) { - seqs[ipos].setDatasetSequence(seq.getDatasetSequence()); + seqipos.setDatasetSequence(seq.getDatasetSequence()); } if (seq.getAnnotation() != null) @@ -300,7 +319,7 @@ public class SequenceGroup implements AnnotatedCollectionI 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) { @@ -318,7 +337,7 @@ public class SequenceGroup implements AnnotatedCollectionI newannot.restrict(startRes, endRes); newannot.setSequenceRef(seqs[ipos]); newannot.adjustForAlignment(); - seqs[ipos].addAlignmentAnnotation(newannot); + seqipos.addAlignmentAnnotation(newannot); } } ipos++; @@ -513,7 +532,7 @@ public class SequenceGroup implements AnnotatedCollectionI */ public Conservation getConservation() { - return conservationData; + return conserve; } /** @@ -524,7 +543,7 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setConservation(Conservation c) { - conservationData = c; + conserve = c; } /** @@ -585,7 +604,7 @@ public class SequenceGroup implements AnnotatedCollectionI */ public boolean recalcConservation() { - return recalcAnnotations(false); + return recalcConservation(false); } /** @@ -597,7 +616,7 @@ public class SequenceGroup implements AnnotatedCollectionI * 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) @@ -617,9 +636,8 @@ public class SequenceGroup implements AnnotatedCollectionI 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) @@ -694,6 +712,8 @@ public class SequenceGroup implements AnnotatedCollectionI c.completeAnnotations(conservation, null, startRes, endRes + 1); } + public ProfilesI consensusData = null; + private void _updateConsensusRow(ProfilesI cnsns, long nseq) { if (consensus == null) @@ -702,7 +722,7 @@ public class SequenceGroup implements AnnotatedCollectionI } 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 @@ -720,12 +740,11 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * 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) { @@ -744,7 +763,7 @@ public class SequenceGroup implements AnnotatedCollectionI // width hmmInformation.setCalcId(InformationThread.HMM_CALC_ID); AAFrequency.completeInformation(hmmInformation, cnsns, startRes, - endRes + 1, nseq, 0f); + endRes + 1); } /** @@ -816,13 +835,16 @@ public class SequenceGroup implements AnnotatedCollectionI /** * Set the first column selected by this group. Runs from 0<=i getHmmSequences() + { + List result = new ArrayList<>(); + for (int i = 0; i < sequences.size(); i++) + { + SequenceI seq = sequences.get(i); + if (seq.hasHMMProfile()) + { + result.add(seq); + } + } + return result; + } + }