X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=a1579c5349d3dd0b0a8390ecd9f998e110fd3c6a;hb=b2b7e99113e1f0962140fc72d989cc826799a2d4;hp=c02a5e3e30d782b88e80c8f76c4e68083c86ee22;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index c02a5e3..a1579c5 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 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. * @@ -22,15 +22,14 @@ package jalview.datamodel; 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 @@ -46,8 +45,6 @@ public class SequenceGroup implements AnnotatedCollectionI Conservation conserve; - Vector aaFrequency; - boolean displayBoxes = true; boolean displayText = true; @@ -74,7 +71,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * Colourscheme applied to group if any */ - public ColourSchemeI cs; + public ResidueShaderI cs; // start column (base 0) int startRes = 0; @@ -121,6 +118,7 @@ public class SequenceGroup implements AnnotatedCollectionI public SequenceGroup() { groupName = "JGroup:" + this.hashCode(); + cs = new ResidueShader(); } /** @@ -141,12 +139,13 @@ public class SequenceGroup implements AnnotatedCollectionI 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(); @@ -159,6 +158,7 @@ public class SequenceGroup implements AnnotatedCollectionI */ public SequenceGroup(SequenceGroup seqsel) { + this(); if (seqsel != null) { sequences = new ArrayList(); @@ -209,7 +209,7 @@ public class SequenceGroup implements AnnotatedCollectionI 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) { @@ -504,32 +504,51 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * 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); @@ -544,17 +563,25 @@ public class SequenceGroup implements AnnotatedCollectionI 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) @@ -577,9 +604,9 @@ public class SequenceGroup implements AnnotatedCollectionI 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) { @@ -894,6 +921,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -906,6 +934,7 @@ public class SequenceGroup implements AnnotatedCollectionI * @param seqrep * the seqrep to set (null means no sequence representative) */ + @Override public void setSeqrep(SequenceI seqrep) { this.seqrep = seqrep; @@ -915,6 +944,7 @@ public class SequenceGroup implements AnnotatedCollectionI * * @return true if group has a sequence representative */ + @Override public boolean hasSeqrep() { return seqrep != null; @@ -1036,7 +1066,8 @@ public class SequenceGroup implements AnnotatedCollectionI /** * - * @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() { @@ -1243,10 +1274,14 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public Iterable findAnnotation(String calcId) { - ArrayList aa = new ArrayList(); + List aa = new ArrayList(); + if (calcId == null) + { + return aa; + } for (AlignmentAnnotation a : getAlignmentAnnotation()) { - if (a.getCalcId() == calcId) + if (calcId.equals(a.getCalcId())) { aa.add(a); } @@ -1331,4 +1366,37 @@ public class SequenceGroup implements AnnotatedCollectionI { return context; } + + 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; + } }