X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=39a1c187827064fc414351c485e0cc212f80241a;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=58dba9d0d605f6f6511411e1e9687fa3164760d9;hpb=4389a166735bf1203894abdf3cf7dd57c4856dbc;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 58dba9d..39a1c18 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -68,6 +68,7 @@ import java.util.BitSet; import java.util.Deque; import java.util.HashMap; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Map; @@ -701,7 +702,8 @@ public abstract class AlignmentViewport * retain any colour thresholds per group while * changing choice of colour scheme (JAL-2386) */ - sg.setColourScheme(cs); + sg.setColourScheme( + cs == null ? null : cs.getInstance(this, sg)); if (cs != null) { sg.getGroupColourScheme().alignmentChanged(sg, @@ -899,18 +901,14 @@ public abstract class AlignmentViewport } } - /** - * trigger update of information annotation - */ @Override - public void updateInformation(final AlignmentViewPanel ap) + public void initInformationWorker(final AlignmentViewPanel ap) { if (calculator .getRegisteredWorkersOfClass(InformationThread.class) == null) { calculator.registerWorker(new InformationThread(this, ap)); } - } // --------START Structure Conservation @@ -1031,17 +1029,17 @@ public abstract class AlignmentViewport /** * should hmm profile be rendered by default */ - protected boolean showHMMSequenceLogo = false; + protected boolean hmmShowSequenceLogo = false; /** * should hmm profile be rendered normalised to row height */ - protected boolean normaliseHMMSequenceLogo = false; + protected boolean hmmNormaliseSequenceLogo = false; /** * should information histograms be rendered by default */ - protected boolean showInformationHistogram = true; + protected boolean hmmShowHistogram = true; /** * @return the showConsensusProfile @@ -1058,7 +1056,7 @@ public abstract class AlignmentViewport @Override public boolean isShowHMMSequenceLogo() { - return showHMMSequenceLogo; + return hmmShowSequenceLogo; } /** @@ -1081,12 +1079,14 @@ public abstract class AlignmentViewport public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo) { - if (showHMMSequenceLogo != this.showHMMSequenceLogo) + if (showHMMSequenceLogo != this.hmmShowSequenceLogo) { - this.showHMMSequenceLogo = showHMMSequenceLogo; - calculator.updateAnnotationFor(InformationThread.class); + this.hmmShowSequenceLogo = showHMMSequenceLogo; + // TODO: updateAnnotation if description (tooltip) will show + // profile in place of information content? + // calculator.updateAnnotationFor(InformationThread.class); } - this.showHMMSequenceLogo = showHMMSequenceLogo; + this.hmmShowSequenceLogo = showHMMSequenceLogo; } /** @@ -1100,11 +1100,10 @@ public abstract class AlignmentViewport /** * @param showInformationHistogram - * the showInformationHistogram to set */ public void setShowInformationHistogram(boolean showInformationHistogram) { - this.showInformationHistogram = showInformationHistogram; + this.hmmShowHistogram = showInformationHistogram; } /** @@ -1160,7 +1159,7 @@ public abstract class AlignmentViewport @Override public boolean isShowInformationHistogram() { - return this.showInformationHistogram; + return this.hmmShowHistogram; } /** @@ -1312,7 +1311,6 @@ public abstract class AlignmentViewport ignoreGapsInConsensusCalculation = b; if (ap != null) { - updateConsensus(ap); if (residueShading != null) { residueShading.setThreshold(residueShading.getThreshold(), @@ -1323,22 +1321,12 @@ public abstract class AlignmentViewport public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap) { - boolean was = ignoreBelowBackGroundFrequencyCalculation; ignoreBelowBackGroundFrequencyCalculation = b; - if (ap != null && was != b) - { - updateInformation(ap); - } } public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap) { - boolean was = infoLetterHeight; infoLetterHeight = b; - if (ap != null && was != b) - { - updateInformation(ap); - } } private long sgrouphash = -1, colselhash = -1; @@ -1749,6 +1737,7 @@ public abstract class AlignmentViewport public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth(), alignment); + isColSelChanged(true); } @Override @@ -1772,7 +1761,8 @@ public abstract class AlignmentViewport } else { - sequences = selectionGroup.getSelectionAsNewSequences(alignment); + sequences = selectionGroup.getSelectionAsNewSequences(alignment, + true); } return sequences; @@ -1854,8 +1844,12 @@ public abstract class AlignmentViewport if (alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns()) { - selection = alignment.getHiddenColumns() - .getVisibleSequenceStrings(start, end, seqs); + for (i = 0; i < iSize; i++) + { + Iterator blocks = alignment.getHiddenColumns() + .getVisContigsIterator(start, end + 1, false); + selection[i] = seqs[i].getSequenceStringFromIterator(blocks); + } } else { @@ -1882,10 +1876,10 @@ public abstract class AlignmentViewport { if (start == 0) { - start = hidden.adjustForHiddenColumns(start); + start = hidden.visibleToAbsoluteColumn(start); } - end = hidden.getHiddenBoundaryRight(start); + end = hidden.getNextHiddenBoundary(false, start); if (start == end) { end = max; @@ -1900,8 +1894,8 @@ public abstract class AlignmentViewport if (hidden != null && hidden.hasHiddenColumns()) { - start = hidden.adjustForHiddenColumns(end); - start = hidden.getHiddenBoundaryLeft(start) + 1; + start = hidden.visibleToAbsoluteColumn(end); + start = hidden.getNextHiddenBoundary(true, start) + 1; } } while (end < max); @@ -1923,13 +1917,13 @@ public abstract class AlignmentViewport AlignmentAnnotation clone = new AlignmentAnnotation(annot); if (selectedOnly && selectionGroup != null) { - alignment.getHiddenColumns().makeVisibleAnnotation( + clone.makeVisibleAnnotation( selectionGroup.getStartRes(), selectionGroup.getEndRes(), - clone); + alignment.getHiddenColumns()); } else { - alignment.getHiddenColumns().makeVisibleAnnotation(clone); + clone.makeVisibleAnnotation(alignment.getHiddenColumns()); } ala.add(clone); } @@ -1962,20 +1956,6 @@ public abstract class AlignmentViewport { alignment.padGaps(); } - if (autoCalculateConsensus) - { - updateConsensus(ap); - } - if (consensusProfiles != null && autoCalculateConsensus) - { - updateConservation(ap); - } - if (autoCalculateStrucConsensus) - { - updateStrucConsensus(ap); - } - // initInformation(); - updateInformation(ap); // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); @@ -1998,7 +1978,6 @@ public abstract class AlignmentViewport updateAllColourSchemes(); calculator.restartWorkers(); - // alignment.adjustSequenceAnnotations(); } /** @@ -2298,7 +2277,7 @@ public abstract class AlignmentViewport sg.setshowSequenceLogo(showprf); sg.setShowConsensusHistogram(showConsHist); sg.setNormaliseSequenceLogo(normLogo); - sg.setshowHMMSequenceLogo(showHMMPrf); + sg.setShowHMMSequenceLogo(showHMMPrf); sg.setShowInformationHistogram(showInfoHist); sg.setNormaliseHMMSequenceLogo(normHMMLogo); } @@ -2904,7 +2883,7 @@ public abstract class AlignmentViewport int lastSeq = alignment.getHeight() - 1; List seqMappings = null; for (int seqNo = ranges - .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) @@ -3085,4 +3064,90 @@ public abstract class AlignmentViewport { return currentTree; } + + @Override + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + + @Override + public boolean isNormaliseHMMSequenceLogo() + { + return hmmNormaliseSequenceLogo; + } + + public void setNormaliseHMMSequenceLogo(boolean state) + { + hmmNormaliseSequenceLogo = state; + } + + /** + * flag set to indicate if structure views might be out of sync with sequences + * in the alignment + */ + + private boolean needToUpdateStructureViews = false; + + @Override + public boolean isUpdateStructures() + { + return needToUpdateStructureViews; + } + + @Override + public void setUpdateStructures(boolean update) + { + needToUpdateStructureViews = update; + } + + @Override + public boolean needToUpdateStructureViews() + { + boolean update = needToUpdateStructureViews; + needToUpdateStructureViews = false; + return update; + } + + @Override + public void addSequenceGroup(SequenceGroup sequenceGroup) + { + alignment.addGroup(sequenceGroup); + + Color col = sequenceGroup.idColour; + if (col != null) + { + col = col.brighter(); + + for (SequenceI sq : sequenceGroup.getSequences()) + { + setSequenceColour(sq, col); + } + } + + if (codingComplement != null) + { + SequenceGroup mappedGroup = MappingUtils + .mapSequenceGroup(sequenceGroup, this, codingComplement); + if (mappedGroup.getSequences().size() > 0) + { + codingComplement.getAlignment().addGroup(mappedGroup); + + if (col != null) + { + for (SequenceI seq : mappedGroup.getSequences()) + { + codingComplement.setSequenceColour(seq, col); + } + } + } + // propagate the structure view update flag according to our own setting + codingComplement.setUpdateStructures(needToUpdateStructureViews); + } + } }