X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=001529900d7b513409be46059a4490887af5903d;hb=bf2dd2a4708bdec06517605f9c6e69bfdc53d5ee;hp=1afe5865135b95d1281aa60637cc73a06f66b234;hpb=86cc86e5815d20b058456c0bf09b979546acde6e;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 1afe586..0015299 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -20,9 +20,19 @@ */ 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.List; +import java.util.Map; + import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; -import jalview.analysis.Profile; import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; @@ -37,14 +47,15 @@ import jalview.datamodel.Annotation; import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenSequences; -import jalview.datamodel.SearchResults; +import jalview.datamodel.ProfilesI; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.schemes.Blosum62ColourScheme; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; -import jalview.schemes.PIDColourScheme; import jalview.structure.CommandListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; @@ -57,17 +68,6 @@ 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 @@ -78,6 +78,8 @@ import java.util.Map; public abstract class AlignmentViewport implements AlignViewportI, CommandListener, VamsasSource { + protected ViewportRanges ranges; + protected ViewStyleI viewStyle = new ViewStyle(); /** @@ -597,7 +599,7 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean ignoreGapsInConsensusCalculation = false; - protected ColourSchemeI globalColourScheme = null; + protected ResidueShaderI residueShading; @Override public void setGlobalColourScheme(ColourSchemeI cs) @@ -605,73 +607,51 @@ public abstract class AlignmentViewport implements AlignViewportI, // TODO: logic refactored from AlignFrame changeColour - // TODO: autorecalc stuff should be changed to rely on the worker system // check to see if we should implement a changeColour(cs) method rather than - // put th logic in here + // put the logic in here // - means that caller decides if they want to just modify state and defer // calculation till later or to do all calculations in thread. // via changecolour - globalColourScheme = cs; - boolean recalc = false; + + /* + * only instantiate alignment colouring once, thereafter update it; + * this means that any conservation or PID threshold settings + * persist when the alignment colour scheme is changed + */ + if (residueShading == null) + { + residueShading = new ResidueShader(viewStyle); + } + residueShading.setColourScheme(cs); + + // TODO: do threshold and increment belong in ViewStyle or ResidueShader? + // ...problem: groups need these, but do not currently have a ViewStyle + if (cs != null) { - cs.setConservationApplied(recalc = getConservationSelected()); - if (getAbovePIDThreshold() || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - recalc = true; - cs.setThreshold(viewStyle.getThreshold(), - ignoreGapsInConsensusCalculation); - } - else - { - cs.setThreshold(0, ignoreGapsInConsensusCalculation); - } - if (recalc) + if (getConservationSelected()) { - cs.setConsensus(hconsensus); - cs.setConservation(hconservation); + residueShading.setConservation(hconservation); } - cs.alignmentChanged(alignment, hiddenRepSequences); + residueShading.alignmentChanged(alignment, hiddenRepSequences); } + + /* + * if 'apply colour to all groups' is selected... do so + * (but don't transfer any colour threshold settings to groups) + */ if (getColourAppliesToAllGroups()) { for (SequenceGroup sg : getAlignment().getGroups()) { - if (cs == null) - { - sg.cs = null; - continue; - } - sg.cs = cs.applyTo(sg, getHiddenRepSequences()); - sg.setConsPercGaps(ConsPercGaps); - if (getAbovePIDThreshold() || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(viewStyle.getThreshold(), - isIgnoreGapsConsensus()); - recalc = true; - } - else - { - sg.cs.setThreshold(0, isIgnoreGapsConsensus()); - } - - if (getConservationSelected()) + /* + * retain any colour thresholds per group while + * changing choice of colour scheme (JAL-2386) + */ + sg.setColourScheme(cs); + if (cs != null) { - sg.cs.setConservationApplied(true); - recalc = true; - } - else - { - sg.cs.setConservation(null); - // sg.cs.setThreshold(0, getIgnoreGapsConsensus()); - } - if (recalc) - { - sg.recalcConservation(); - } - else - { - sg.cs.alignmentChanged(sg, hiddenRepSequences); + sg.getGroupColourScheme() + .alignmentChanged(sg, hiddenRepSequences); } } } @@ -680,13 +660,22 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { - return globalColourScheme; + return residueShading == null ? null : residueShading + .getColourScheme(); + } + + @Override + public ResidueShaderI getResidueShading() + { + return residueShading; } protected AlignmentAnnotation consensus; protected AlignmentAnnotation complementConsensus; + protected AlignmentAnnotation gapcounts; + protected AlignmentAnnotation strucConsensus; protected AlignmentAnnotation conservation; @@ -700,7 +689,7 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * results of alignment consensus analysis for visible portion of view */ - protected Profile[] hconsensus = null; + protected ProfilesI hconsensus = null; /** * results of cDNA complement consensus visible portion of view @@ -734,7 +723,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public void setSequenceConsensusHash(Profile[] hconsensus) + public void setSequenceConsensusHash(ProfilesI hconsensus) { this.hconsensus = hconsensus; } @@ -746,7 +735,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public Profile[] getSequenceConsensusHash() + public ProfilesI getSequenceConsensusHash() { return hconsensus; } @@ -789,6 +778,12 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public AlignmentAnnotation getAlignmentGapAnnotation() + { + return gapcounts; + } + + @Override public AlignmentAnnotation getComplementConsensusAnnotation() { return complementConsensus; @@ -940,7 +935,7 @@ public abstract class AlignmentViewport implements AlignViewportI, hconsensus = null; hcomplementConsensus = null; // colour scheme may hold reference to consensus - globalColourScheme = null; + residueShading = null; // TODO remove listeners from changeSupport? changeSupport = null; setAlignment(null); @@ -1088,7 +1083,8 @@ public abstract class AlignmentViewport implements AlignViewportI, } /** - * Set the selection group for this window. + * Set the selection group for this window. Also sets the current alignment as + * the context for the group, if it does not already have one. * * @param sg * - group holding references to sequences in this alignment view @@ -1098,6 +1094,10 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setSelectionGroup(SequenceGroup sg) { selectionGroup = sg; + if (sg != null && sg.getContext() == null) + { + sg.setContext(alignment); + } } public void setHiddenColumns(ColumnSelection colsel) @@ -1210,9 +1210,9 @@ public abstract class AlignmentViewport implements AlignViewportI, if (ap != null) { updateConsensus(ap); - if (globalColourScheme != null) + if (residueShading != null) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + residueShading.setThreshold(residueShading.getThreshold(), ignoreGapsInConsensusCalculation); } } @@ -1284,6 +1284,8 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean showConsensus = true; + protected boolean showOccupancy = true; + private Map sequenceColours = new HashMap(); protected SequenceAnnotationOrder sortAnnotationsBy = null; @@ -1295,15 +1297,6 @@ public abstract class AlignmentViewport implements AlignViewportI, */ 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 * @@ -1848,7 +1841,7 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.setEndRes(alWidth - 1); } - resetAllColourSchemes(); + updateAllColourSchemes(); calculator.restartWorkers(); // alignment.adjustSequenceAnnotations(); } @@ -1856,17 +1849,17 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * reset scope and do calculations for all applied colourschemes on alignment */ - void resetAllColourSchemes() + void updateAllColourSchemes() { - ColourSchemeI cs = globalColourScheme; - if (cs != null) + ResidueShaderI rs = residueShading; + if (rs != null) { - cs.alignmentChanged(alignment, hiddenRepSequences); + rs.alignmentChanged(alignment, hiddenRepSequences); - cs.setConsensus(hconsensus); - if (cs.conservationApplied()) + rs.setConsensus(hconsensus); + if (rs.conservationApplied()) { - cs.setConservation(Conservation.calculateConservation("All", 3, + rs.setConservation(Conservation.calculateConservation("All", alignment.getSequences(), 0, alignment.getWidth(), false, getConsPercGaps(), false)); } @@ -1902,16 +1895,17 @@ public abstract class AlignmentViewport implements AlignViewportI, consensus = new AlignmentAnnotation("Consensus", "PID", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(consensus); + initGapCounts(); initComplementConsensus(); } } /** - * If this is a protein alignment and there are mappings to cDNA, add the cDNA - * consensus annotation. + * If this is a protein alignment and there are mappings to cDNA, adds the + * cDNA consensus annotation and returns true, else returns false. */ - public void initComplementConsensus() + public boolean initComplementConsensus() { if (!alignment.isNucleotide()) { @@ -1938,9 +1932,11 @@ public abstract class AlignmentViewport implements AlignViewportI, "PID for cDNA", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(complementConsensus); + return true; } } } + return false; } private void initConsensus(AlignmentAnnotation aa) @@ -1954,6 +1950,24 @@ public abstract class AlignmentViewport implements AlignViewportI, } } + // these should be extracted from the view model - style and settings for + // derived annotation + private void initGapCounts() + { + if (showOccupancy) + { + gapcounts = new AlignmentAnnotation("Occupancy", + "Number of aligned positions", new Annotation[1], 0f, + alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH); + gapcounts.hasText = true; + gapcounts.autoCalculated = true; + gapcounts.scaleColLabel = true; + gapcounts.graph = AlignmentAnnotation.BAR_GRAPH; + + alignment.addAnnotation(gapcounts); + } + } + private void initConservation() { if (showConservation) @@ -2440,6 +2454,11 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setViewStyle(ViewStyleI settingsForView) { viewStyle = new ViewStyle(settingsForView); + if (residueShading != null) + { + residueShading.setConservationApplied(settingsForView + .isConservationColourSelected()); + } } @Override @@ -2650,63 +2669,10 @@ public abstract class AlignmentViewport implements AlignViewportI, this.followHighlight = b; } - public int getStartRes() - { - return startRes; - } - @Override - public int getEndRes() - { - return endRes; - } - - public int getStartSeq() - { - return startSeq; - } - - public void setStartRes(int res) + public ViewportRanges getRanges() { - 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; + return ranges; } /** @@ -2717,7 +2683,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * the SearchResults to add to * @return the offset (below top of visible region) of the matched sequence */ - protected int findComplementScrollTarget(SearchResults sr) + protected int findComplementScrollTarget(SearchResultsI sr) { final AlignViewportI complement = getCodingComplement(); if (complement == null || !complement.isFollowHighlight()) @@ -2746,7 +2712,8 @@ public abstract class AlignmentViewport implements AlignViewportI, * locate 'middle' column (true middle if an odd number visible, left of * middle if an even number visible) */ - int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2; + int middleColumn = ranges.getStartRes() + + (ranges.getEndRes() - ranges.getStartRes()) / 2; final HiddenSequences hiddenSequences = getAlignment() .getHiddenSequences(); @@ -2756,7 +2723,7 @@ public abstract class AlignmentViewport implements AlignViewportI, */ int lastSeq = alignment.getHeight() - 1; List seqMappings = null; - for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) @@ -2847,4 +2814,27 @@ public abstract class AlignmentViewport implements AlignViewportI, return selectionGroup.getContext() == alignment || selectionIsDefinedGroup; } + + /** + * null, or currently highlighted results on this view + */ + private SearchResultsI searchResults = null; + + @Override + public boolean hasSearchResults() + { + return searchResults != null; + } + + @Override + public void setSearchResults(SearchResultsI results) + { + searchResults = results; + } + + @Override + public SearchResultsI getSearchResults() + { + return searchResults; + } }