X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=72eb9c0e104f68a331ed8ae0af83af05b76e04e6;hb=e9b0f1619b7b33b9d2ebb3f64d7cefe563c24db8;hp=1ae879b0b4bfc545392c9d7371cfffd84f4f0d31;hpb=1f0742002d457b49733648b9369922bb0b78d2f0;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 1ae879b..72eb9c0 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -20,10 +20,23 @@ */ package jalview.viewmodel; +import java.awt.Color; +import java.beans.PropertyChangeSupport; +import java.util.ArrayDeque; +import java.util.ArrayList; +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; + import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; import jalview.analysis.TreeModel; import jalview.api.AlignCalcManagerI; +import jalview.api.AlignExportSettingsI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeaturesDisplayedI; @@ -31,6 +44,7 @@ import jalview.api.ViewStyleI; import jalview.commands.CommandI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentExportData; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; @@ -59,18 +73,6 @@ import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; -import java.awt.Color; -import java.beans.PropertyChangeSupport; -import java.util.ArrayDeque; -import java.util.ArrayList; -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; - /** * base class holding visualization and analysis attributes and common logic for * an active alignment view displayed in the GUI @@ -569,6 +571,28 @@ public abstract class AlignmentViewport viewStyle.setSeqNameItalics(default1); } + /** + * Set the flag indicating that feature count annotation tracks are to be + * displayed + * + * @see jalview.api.ViewStyleI#setShowSequenceFeatureCounts(boolean) + */ + @Override + public void setShowSequenceFeatureCounts(boolean show) + { + viewStyle.setShowSequenceFeatureCounts(show); + } + + /** + * @return true if feature count annotation tracks are to be displayed + * @see jalview.api.ViewStyleI#isShowSequenceFeatureCounts() + */ + @Override + public boolean isShowSequenceFeatureCounts() + { + return viewStyle.isShowSequenceFeatureCounts(); + } + @Override public AlignmentI getAlignment() { @@ -662,7 +686,7 @@ 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, @@ -708,13 +732,13 @@ public abstract class AlignmentViewport /** * results of cDNA complement consensus visible portion of view */ - protected Hashtable[] hcomplementConsensus = null; + protected Hashtable[] hcomplementConsensus = null; /** * results of secondary structure base pair consensus for visible portion of * view */ - protected Hashtable[] hStrucConsensus = null; + protected Hashtable[] hStrucConsensus = null; protected Conservation hconservation = null; @@ -743,7 +767,8 @@ public abstract class AlignmentViewport } @Override - public void setComplementConsensusHash(Hashtable[] hconsensus) + public void setComplementConsensusHash( + Hashtable[] hconsensus) { this.hcomplementConsensus = hconsensus; } @@ -755,19 +780,20 @@ public abstract class AlignmentViewport } @Override - public Hashtable[] getComplementConsensusHash() + public Hashtable[] getComplementConsensusHash() { return hcomplementConsensus; } @Override - public Hashtable[] getRnaStructureConsensusHash() + public Hashtable[] getRnaStructureConsensusHash() { return hStrucConsensus; } @Override - public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus) + public void setRnaStructureConsensusHash( + Hashtable[] hStrucConsensus) { this.hStrucConsensus = hStrucConsensus; @@ -958,6 +984,7 @@ public abstract class AlignmentViewport ranges = null; currentTree = null; selectionGroup = null; + colSel = null; setAlignment(null); } @@ -1636,6 +1663,7 @@ public abstract class AlignmentViewport public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth(), alignment); + isColSelChanged(true); } @Override @@ -1796,7 +1824,7 @@ public abstract class AlignmentViewport } } while (end < max); - int[][] startEnd = new int[regions.size()][2]; + // int[][] startEnd = new int[regions.size()][2]; return regions; } @@ -1814,9 +1842,8 @@ public abstract class AlignmentViewport AlignmentAnnotation clone = new AlignmentAnnotation(annot); if (selectedOnly && selectionGroup != null) { - clone.makeVisibleAnnotation( - selectionGroup.getStartRes(), selectionGroup.getEndRes(), - alignment.getHiddenColumns()); + clone.makeVisibleAnnotation(selectionGroup.getStartRes(), + selectionGroup.getEndRes(), alignment.getHiddenColumns()); } else { @@ -2151,7 +2178,7 @@ public abstract class AlignmentViewport * TODO reorder the annotation rows according to group/sequence ordering on * alignment */ - boolean sortg = true; + // boolean sortg = true; // remove old automatic annotation // add any new annotation @@ -2261,7 +2288,7 @@ public abstract class AlignmentViewport public void clearSequenceColours() { sequenceColours.clear(); - }; + } @Override public AlignViewportI getCodingComplement() @@ -2978,4 +3005,117 @@ public abstract class AlignmentViewport { return currentTree; } + + @Override + public AlignmentExportData getAlignExportData( + AlignExportSettingsI options) + { + AlignmentI alignmentToExport = null; + String[] omitHidden = null; + alignmentToExport = null; + + if (hasHiddenColumns() && !options.isExportHiddenColumns()) + { + omitHidden = getViewAsString(false, + options.isExportHiddenSequences()); + } + + int[] alignmentStartEnd = new int[2]; + if (hasHiddenRows() && options.isExportHiddenSequences()) + { + alignmentToExport = getAlignment().getHiddenSequences() + .getFullAlignment(); + } + else + { + alignmentToExport = getAlignment(); + } + alignmentStartEnd = getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, + omitHidden, alignmentStartEnd); + return ed; + } + + /** + * 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); + } + } + + @Override + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) + { + int start = 0; + int end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + end = alignment.getWidth(); + } + return (alignment.getHiddenColumns().getVisContigsIterator(start, end, + false)); + } }