X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=463b909ad8ef1c96ba00c06f208f1e056548e25d;hb=ba61fc7a3397ce6b57640e0b19c76392a983768a;hp=8218ba7729231f689da37d187688d614164cb988;hpb=244520d01226040ec02eb8560bf0b181932797cf;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 8218ba7..463b909 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -22,8 +22,8 @@ package jalview.datamodel; import jalview.analysis.AAFrequency; import jalview.analysis.Conservation; -import jalview.schemes.CollectionColourScheme; -import jalview.schemes.CollectionColourSchemeI; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; import java.awt.Color; @@ -52,6 +52,12 @@ public class SequenceGroup implements AnnotatedCollectionI 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; @@ -59,7 +65,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * group members */ - private List sequences = new ArrayList(); + private List sequences = new ArrayList<>(); /** * representative sequence for this group (if any) @@ -71,7 +77,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * Colourscheme applied to group if any */ - public CollectionColourSchemeI cs; + public ResidueShaderI cs; // start column (base 0) int startRes = 0; @@ -104,13 +110,23 @@ public class SequenceGroup implements AnnotatedCollectionI */ 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. @@ -118,7 +134,7 @@ public class SequenceGroup implements AnnotatedCollectionI public SequenceGroup() { groupName = "JGroup:" + this.hashCode(); - cs = new CollectionColourScheme(); + cs = new ResidueShader(); } /** @@ -145,7 +161,7 @@ public class SequenceGroup implements AnnotatedCollectionI this.displayBoxes = displayBoxes; this.displayText = displayText; this.colourText = colourText; - this.cs = new CollectionColourScheme(scheme); + this.cs = new ResidueShader(scheme); startRes = start; endRes = end; recalcConservation(); @@ -161,7 +177,7 @@ public class SequenceGroup implements AnnotatedCollectionI this(); if (seqsel != null) { - sequences = new ArrayList(); + sequences = new ArrayList<>(); sequences.addAll(seqsel.sequences); if (seqsel.groupName != null) { @@ -172,13 +188,17 @@ public class SequenceGroup implements AnnotatedCollectionI colourText = seqsel.colourText; startRes = seqsel.startRes; endRes = seqsel.endRes; - cs = seqsel.cs; + cs = new ResidueShader(seqsel.getColourScheme()); 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; @@ -195,6 +215,11 @@ public class SequenceGroup implements AnnotatedCollectionI } } + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + public SequenceI[] getSelectionAsNewSequences(AlignmentI align) { int iSize = sequences.size(); @@ -311,7 +336,7 @@ public class SequenceGroup implements AnnotatedCollectionI } else { - List allSequences = new ArrayList(); + List allSequences = new ArrayList<>(); for (SequenceI seq : sequences) { allSequences.add(seq); @@ -951,11 +976,6 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * 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. * @@ -977,11 +997,6 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * visibility of columns intersecting this group - */ - private boolean hidecols = false; - - /** * set intended visibility of columns covered by this group * * @param visibility @@ -1015,7 +1030,7 @@ public class SequenceGroup implements AnnotatedCollectionI { SequenceGroup sgroup = new SequenceGroup(this); SequenceI[] insect = getSequencesInOrder(alignment); - sgroup.sequences = new ArrayList(); + sgroup.sequences = new ArrayList<>(); for (int s = 0; insect != null && s < insect.length; s++) { if (map == null || map.containsKey(insect[s])) @@ -1043,13 +1058,6 @@ public class SequenceGroup implements AnnotatedCollectionI 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 @@ -1242,7 +1250,7 @@ public class SequenceGroup implements AnnotatedCollectionI { // TODO add in other methods like 'getAlignmentAnnotation(String label), // etc' - ArrayList annot = new ArrayList(); + ArrayList annot = new ArrayList<>(); synchronized (sequences) { for (SequenceI seq : sequences) @@ -1274,7 +1282,7 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public Iterable findAnnotation(String calcId) { - List aa = new ArrayList(); + List aa = new ArrayList<>(); if (calcId == null) { return aa; @@ -1289,22 +1297,18 @@ public class SequenceGroup implements AnnotatedCollectionI return aa; } - /** - * Returns a list of annotations that match the specified sequenceRef, calcId - * and label, ignoring null values. - * - * @return list of AlignmentAnnotation objects - */ @Override public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList(); + ArrayList aa = new ArrayList<>(); 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)) + if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId() + .equals(calcId))) + && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq)) + && (label == null || (ann.label != null && ann.label + .equals(label)))) { aa.add(ann); } @@ -1344,16 +1348,45 @@ public class SequenceGroup implements AnnotatedCollectionI } } - 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; } /* @@ -1367,16 +1400,21 @@ public class SequenceGroup implements AnnotatedCollectionI return context; } + public boolean isDefined() + { + return isDefined; + } + public void setColourScheme(ColourSchemeI scheme) { if (cs == null) { - cs = new CollectionColourScheme(); + cs = new ResidueShader(); } cs.setColourScheme(scheme); } - public void setGroupColourScheme(CollectionColourSchemeI scheme) + public void setGroupColourScheme(ResidueShaderI scheme) { cs = scheme; } @@ -1386,7 +1424,7 @@ public class SequenceGroup implements AnnotatedCollectionI return cs == null ? null : cs.getColourScheme(); } - public CollectionColourSchemeI getGroupColourScheme() + public ResidueShaderI getGroupColourScheme() { return cs; } @@ -1394,10 +1432,29 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public boolean isNucleotide() { - if (context != null && context instanceof AlignmentI) - { - return ((AlignmentI) context).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); + } }