X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=899e8a7872378e10e5c66264e71ebda022f3da04;hb=b4abe1ffdea4b7711cdc72c6c95af4356187302b;hp=7054ed3d068efc7bb2640fff3724fffdbf1dce09;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 7054ed3..899e8a7 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -20,17 +20,6 @@ */ package jalview.viewmodel; -import java.awt.Color; -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.List; -import java.util.Map; -import java.util.Set; - import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; @@ -46,6 +35,8 @@ import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.SearchResults; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; @@ -57,12 +48,25 @@ import jalview.schemes.ResidueProperties; import jalview.structure.CommandListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.util.Comparison; +import jalview.util.MappingUtils; import jalview.viewmodel.styles.ViewStyle; import jalview.workers.AlignCalcManager; import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; +import java.awt.Color; +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.List; +import java.util.Map; +import java.util.Set; + /** * base class holding visualization and analysis attributes and common logic for * an active alignment view displayed in the GUI @@ -71,7 +75,7 @@ import jalview.workers.StrucConsensusThread; * */ public abstract class AlignmentViewport implements AlignViewportI, - ViewStyleI, CommandListener, VamsasSource + CommandListener, VamsasSource { protected ViewStyleI viewStyle = new ViewStyle(); @@ -502,15 +506,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } /** - * @param selected - * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean) - */ - public void setShowSeqFeaturesHeight(boolean selected) - { - viewStyle.setShowSeqFeaturesHeight(selected); - } - - /** * alignment displayed in the viewport. Please use get/setter */ protected AlignmentI alignment; @@ -1060,14 +1055,13 @@ public abstract class AlignmentViewport implements AlignViewportI, // hasHiddenColumns = colSel.hasHiddenColumns(); } - protected boolean hasHiddenRows = false; - @Override public boolean hasHiddenRows() { - return hasHiddenRows; + return alignment.getHiddenSequences().getSize() > 0; } + protected SequenceGroup selectionGroup; public void setSequenceSetId(String newid) @@ -1196,6 +1190,20 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean showAutocalculatedAbove; /** + * when set, view will scroll to show the highlighted position + */ + private boolean followHighlight = true; + + // TODO private with getters and setters? + public int startRes; + + public int endRes; + + public int startSeq; + + public int endSeq; + + /** * Property change listener for changes in alignment * * @param listener @@ -1290,7 +1298,6 @@ public abstract class AlignmentViewport implements AlignViewportI, setSequenceAnnotationsVisible(seq, true); } - hasHiddenRows = false; hiddenRepSequences = null; firePropertyChange("alignment", null, alignment.getSequences()); @@ -1318,12 +1325,6 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.addSequence(seq, false); setSequenceAnnotationsVisible(seq, true); } - // JBPNote: refactor: only update flag if we modified visiblity (used to - // do this regardless) - if (alignment.getHiddenSequences().getSize() < 1) - { - hasHiddenRows = false; - } firePropertyChange("alignment", null, alignment.getSequences()); sendSelection(); } @@ -1352,7 +1353,6 @@ public abstract class AlignmentViewport implements AlignViewportI, alignment.getHiddenSequences().hideSequence(seq[i]); setSequenceAnnotationsVisible(seq[i], false); } - hasHiddenRows = true; firePropertyChange("alignment", null, alignment.getSequences()); } } @@ -1731,7 +1731,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * If this is a protein alignment and there are mappings to cDNA, add the cDNA * consensus annotation. */ - protected void initComplementConsensus() + public void initComplementConsensus() { if (!alignment.isNucleotide()) { @@ -2075,7 +2075,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public void setShowSequenceFeaturesHeight(boolean selected) { - viewStyle.setShowSeqFeaturesHeight(selected); + viewStyle.setShowSequenceFeaturesHeight(selected); } @Override @@ -2175,14 +2175,6 @@ public abstract class AlignmentViewport implements AlignViewportI, { return viewStyle.isShowColourText(); } - /** - * @return - * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight() - */ - public boolean isShowSeqFeaturesHeight() - { - return viewStyle.isShowSeqFeaturesHeight(); - } /** * @param conservationColourSelected @@ -2411,4 +2403,162 @@ public abstract class AlignmentViewport implements AlignViewportI, { this.showAutocalculatedAbove = showAutocalculatedAbove; } + + @Override + public boolean isScaleProteinAsCdna() + { + return viewStyle.isScaleProteinAsCdna(); + } + + @Override + public void setScaleProteinAsCdna(boolean b) + { + viewStyle.setScaleProteinAsCdna(b); + } + + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ + @Override + public final boolean isFollowHighlight() + { + return followHighlight; + } + + @Override + public final void setFollowHighlight(boolean b) + { + this.followHighlight = b; + } + + public int getStartRes() + { + return startRes; + } + + public int getEndRes() + { + return endRes; + } + + public int getStartSeq() + { + return startSeq; + } + + public void setStartRes(int res) + { + this.startRes = res; + } + + public void setStartSeq(int seq) + { + this.startSeq = seq; + } + + public void setEndRes(int res) + { + if (res > alignment.getWidth() - 1) + { + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); + res = alignment.getWidth() - 1; + } + if (res < 0) + { + res = 0; + } + this.endRes = res; + } + + public void setEndSeq(int seq) + { + if (seq > alignment.getHeight()) + { + seq = alignment.getHeight(); + } + if (seq < 0) + { + seq = 0; + } + this.endSeq = seq; + } + + public int getEndSeq() + { + return endSeq; + } + + /** + * Helper method to populate the SearchResults with the location in the + * complementary alignment to scroll to, in order to match this one. + * + * @param sr + * the SearchResults to add to + * @return the offset (below top of visible region) of the matched sequence + */ + protected int findComplementScrollTarget(SearchResults sr) + { + final AlignViewportI complement = getCodingComplement(); + if (complement == null || !complement.isFollowHighlight()) + { + return 0; + } + boolean iAmProtein = !getAlignment().isNucleotide(); + AlignmentI proteinAlignment = iAmProtein ? getAlignment() + : complement.getAlignment(); + if (proteinAlignment == null) + { + return 0; + } + final Set mappings = proteinAlignment + .getCodonFrames(); + + /* + * Heuristic: find the first mapped sequence (if any) with a non-gapped + * residue in the middle column of the visible region. Scroll the + * complementary alignment to line up the corresponding residue. + */ + int seqOffset = 0; + SequenceI sequence = null; + + /* + * locate 'middle' column (true middle if an odd number visible, left of + * middle if an even number visible) + */ + int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2; + final HiddenSequences hiddenSequences = getAlignment() + .getHiddenSequences(); + for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++) + { + sequence = getAlignment().getSequenceAt(seqNo); + if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) + { + continue; + } + if (Comparison.isGap(sequence.getCharAt(middleColumn))) + { + continue; + } + List seqMappings = MappingUtils + .findMappingsForSequence(sequence, mappings); + if (!seqMappings.isEmpty()) + { + break; + } + } + + if (sequence == null) + { + /* + * No ungapped mapped sequence in middle column - do nothing + */ + return 0; + } + MappingUtils.addSearchResults(sr, sequence, + sequence.findPosition(middleColumn), mappings); + return seqOffset; + } }