X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=3e1bc631db3679f770558aa9f3ef465f425ee483;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=a0cbff48c46e79b5384dbcdc14264fcb5b37c965;hpb=ea2cf1fb34a7630388e87c058d994d2a4017f9e3;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index a0cbff4..3e1bc63 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -20,21 +20,38 @@ */ 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; import jalview.api.ViewStyleI; +import jalview.bin.Console; 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; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; import jalview.datamodel.ProfilesI; @@ -43,6 +60,8 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.QuitHandler; +import jalview.project.Jalview2XML; import jalview.renderer.ResidueShader; import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; @@ -59,17 +78,6 @@ 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.List; -import java.util.Map; - /** * base class holding visualization and analysis attributes and common logic for * an active alignment view displayed in the GUI @@ -97,6 +105,11 @@ public abstract class AlignmentViewport protected Deque redoList = new ArrayDeque<>(); /** + * used to determine if quit should be confirmed + */ + private boolean savedUpToDate = false; + + /** * alignment displayed in the viewport. Please use get/setter */ protected AlignmentI alignment; @@ -661,7 +674,7 @@ 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, @@ -707,13 +720,13 @@ 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; @@ -742,7 +755,8 @@ public abstract class AlignmentViewport } @Override - public void setComplementConsensusHash(Hashtable[] hconsensus) + public void setComplementConsensusHash( + Hashtable[] hconsensus) { this.hcomplementConsensus = hconsensus; } @@ -754,19 +768,20 @@ 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; @@ -919,7 +934,8 @@ public abstract class AlignmentViewport } if (calculator.workingInvolvedWith(alignmentAnnotation)) { - // System.err.println("grey out ("+alignmentAnnotation.label+")"); + // jalview.bin.Console.errPrintln("grey out + // ("+alignmentAnnotation.label+")"); return true; } return false; @@ -957,6 +973,7 @@ public abstract class AlignmentViewport ranges = null; currentTree = null; selectionGroup = null; + colSel = null; setAlignment(null); } @@ -1191,7 +1208,7 @@ public abstract class AlignmentViewport { if (sequenceSetID != null) { - System.err.println( + jalview.bin.Console.errPrintln( "Warning - overwriting a sequenceSetId for a viewport!"); } sequenceSetID = new String(newid); @@ -1635,6 +1652,7 @@ public abstract class AlignmentViewport public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth(), alignment); + isColSelChanged(true); } @Override @@ -1740,8 +1758,12 @@ 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 { @@ -1768,10 +1790,10 @@ 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; @@ -1786,12 +1808,12 @@ 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); - int[][] startEnd = new int[regions.size()][2]; + // int[][] startEnd = new int[regions.size()][2]; return regions; } @@ -1809,13 +1831,12 @@ public abstract class AlignmentViewport AlignmentAnnotation clone = new AlignmentAnnotation(annot); if (selectedOnly && selectionGroup != null) { - alignment.getHiddenColumns().makeVisibleAnnotation( - selectionGroup.getStartRes(), selectionGroup.getEndRes(), - clone); + clone.makeVisibleAnnotation(selectionGroup.getStartRes(), + selectionGroup.getEndRes(), alignment.getHiddenColumns()); } else { - alignment.getHiddenColumns().makeVisibleAnnotation(clone); + clone.makeVisibleAnnotation(alignment.getHiddenColumns()); } ala.add(clone); } @@ -2080,7 +2101,7 @@ public abstract class AlignmentViewport { if (aa == null) { - System.err.println("Null annotation row: ignoring."); + jalview.bin.Console.errPrintln("Null annotation row: ignoring."); continue; } if (!aa.visible) @@ -2112,7 +2133,7 @@ public abstract class AlignmentViewport if (aa.graph > 0) { - aa.height += aa.graphHeight; + aa.height += aa.graphHeight + 20; } if (aa.height == 0) @@ -2146,7 +2167,7 @@ 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 @@ -2256,7 +2277,7 @@ public abstract class AlignmentViewport public void clearSequenceColours() { sequenceColours.clear(); - }; + } @Override public AlignViewportI getCodingComplement() @@ -2273,7 +2294,8 @@ public abstract class AlignmentViewport { if (this == av) { - System.err.println("Ignoring recursive setCodingComplement request"); + jalview.bin.Console + .errPrintln("Ignoring recursive setCodingComplement request"); } else { @@ -2604,6 +2626,8 @@ public abstract class AlignmentViewport { this.historyList.push(command); broadcastCommand(command, false); + setSavedUpToDate(false); + Jalview2XML.setStateSavedUpToDate(false); } } @@ -2709,6 +2733,30 @@ public abstract class AlignmentViewport viewStyle.setProteinFontAsCdna(b); } + @Override + public void setShowComplementFeatures(boolean b) + { + viewStyle.setShowComplementFeatures(b); + } + + @Override + public boolean isShowComplementFeatures() + { + return viewStyle.isShowComplementFeatures(); + } + + @Override + public void setShowComplementFeaturesOnTop(boolean b) + { + viewStyle.setShowComplementFeaturesOnTop(b); + } + + @Override + public boolean isShowComplementFeaturesOnTop() + { + return viewStyle.isShowComplementFeaturesOnTop(); + } + /** * @return true if view should scroll to show the highlighted region of a * sequence @@ -2781,7 +2829,7 @@ 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)) @@ -2897,6 +2945,19 @@ public abstract class AlignmentViewport return searchResults; } + @Override + public ContactListI getContactList(AlignmentAnnotation _aa, int column) + { + return alignment.getContactListFor(_aa, column); + } + + @Override + public ContactMatrixI getContactMatrix( + AlignmentAnnotation alignmentAnnotation) + { + return alignment.getContactMatrixFor(alignmentAnnotation); + } + /** * get the consensus sequence as displayed under the PID consensus annotation * row. @@ -2949,4 +3010,137 @@ 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)); + } + + public void setSavedUpToDate(boolean s) + { + setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES); + } + + public void setSavedUpToDate(boolean s, QuitHandler.Message m) + { + Console.debug( + "Setting " + this.getViewId() + " setSavedUpToDate to " + s); + savedUpToDate = s; + QuitHandler.setMessage(m); + } + + public boolean savedUpToDate() + { + Console.debug("Returning " + this.getViewId() + " savedUpToDate value: " + + savedUpToDate); + return savedUpToDate; + } }