X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=8d2580b93833f17e643daf2b296da8fa3e0e817b;hb=00b6a6802349029e2c6fb3263201287ba921dd63;hp=69879b75fe64a5073bc18c9604944273d50d5810;hpb=b0832234b2a89510d715951d94ae213e449ca6b2;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 69879b7..8d2580b 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -20,6 +20,17 @@ */ 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.api.AlignCalcManagerI; @@ -42,11 +53,9 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.schemes.Blosum62ColourScheme; -import jalview.schemes.CollectionColourScheme; -import jalview.schemes.CollectionColourSchemeI; +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; @@ -59,17 +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 @@ -80,6 +78,8 @@ import java.util.Map; public abstract class AlignmentViewport implements AlignViewportI, CommandListener, VamsasSource { + protected ViewportRanges ranges; + protected ViewStyleI viewStyle = new ViewStyle(); /** @@ -599,7 +599,7 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean ignoreGapsInConsensusCalculation = false; - protected CollectionColourSchemeI globalColourScheme; + protected ResidueShaderI residueShading; @Override public void setGlobalColourScheme(ColourSchemeI cs) @@ -607,37 +607,32 @@ 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 /* - * only instantiate collection colour scheme once, thereafter update it + * 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 (globalColourScheme == null) + if (residueShading == null) { - globalColourScheme = new CollectionColourScheme(); + residueShading = new ResidueShader(viewStyle); } - globalColourScheme.setColourScheme(cs); + residueShading.setColourScheme(cs); - // boolean recalc = false; - // TODO: do threshold and increment belong in ViewStyle or colour scheme? - // problem: groups need this but do not currently have a ViewStyle + // TODO: do threshold and increment belong in ViewStyle or ResidueShader? + // ...problem: groups need these, but do not currently have a ViewStyle if (cs != null) { - if (getConservationSelected() || getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) + if (getConservationSelected()) { - globalColourScheme.setConservation(hconservation); - globalColourScheme - .setConservationApplied(getConservationSelected()); + residueShading.setConservation(hconservation); } - globalColourScheme.alignmentChanged(alignment, hiddenRepSequences); + residueShading.alignmentChanged(alignment, hiddenRepSequences); } /* @@ -665,20 +660,22 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { - return globalColourScheme == null ? null : globalColourScheme + return residueShading == null ? null : residueShading .getColourScheme(); } @Override - public CollectionColourSchemeI getViewportColourScheme() + public ResidueShaderI getResidueShading() { - return globalColourScheme; + return residueShading; } protected AlignmentAnnotation consensus; protected AlignmentAnnotation complementConsensus; + protected AlignmentAnnotation gapcounts; + protected AlignmentAnnotation strucConsensus; protected AlignmentAnnotation conservation; @@ -781,6 +778,12 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public AlignmentAnnotation getAlignmentGapAnnotation() + { + return gapcounts; + } + + @Override public AlignmentAnnotation getComplementConsensusAnnotation() { return complementConsensus; @@ -820,7 +823,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public void updateConsensus(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if (consensus == null || !autoCalculateConsensus) + if ((consensus == null || gapcounts == null) || !autoCalculateConsensus) { return; } @@ -932,7 +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); @@ -1080,7 +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 @@ -1090,6 +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) @@ -1202,9 +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); } } @@ -1287,15 +1295,6 @@ 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 * @@ -1840,7 +1839,7 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.setEndRes(alWidth - 1); } - resetAllColourSchemes(); + updateAllColourSchemes(); calculator.restartWorkers(); // alignment.adjustSequenceAnnotations(); } @@ -1848,17 +1847,17 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * reset scope and do calculations for all applied colourschemes on alignment */ - void resetAllColourSchemes() + void updateAllColourSchemes() { - CollectionColourSchemeI 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", + rs.setConservation(Conservation.calculateConservation("All", alignment.getSequences(), 0, alignment.getWidth(), false, getConsPercGaps(), false)); } @@ -1894,16 +1893,21 @@ public abstract class AlignmentViewport implements AlignViewportI, consensus = new AlignmentAnnotation("Consensus", "PID", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(consensus); + gapcounts = new AlignmentAnnotation("Occupancy", + "Number of aligned positions", + new Annotation[1], 0f, alignment.getHeight(), + AlignmentAnnotation.BAR_GRAPH); + initGapCounts(gapcounts); 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()) { @@ -1930,9 +1934,11 @@ 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) @@ -1946,6 +1952,21 @@ public abstract class AlignmentViewport implements AlignViewportI, } } + // these should be extracted from the view model - style and settings for + // derived annotation + private void initGapCounts(AlignmentAnnotation counts) + { + counts.hasText = true; + counts.autoCalculated = true; + counts.scaleColLabel = true; + counts.graph = AlignmentAnnotation.BAR_GRAPH; + + if (showConsensus) + { + alignment.addAnnotation(counts); + } + } + private void initConservation() { if (showConservation) @@ -2432,6 +2453,11 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setViewStyle(ViewStyleI settingsForView) { viewStyle = new ViewStyle(settingsForView); + if (residueShading != null) + { + residueShading.setConservationApplied(settingsForView + .isConservationColourSelected()); + } } @Override @@ -2642,63 +2668,10 @@ 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) - { - this.startRes = res; - } - - public void setStartSeq(int seq) + public ViewportRanges getRanges() { - 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; } /** @@ -2738,7 +2711,8 @@ 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(); @@ -2748,7 +2722,7 @@ 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)) @@ -2816,7 +2790,6 @@ public abstract class AlignmentViewport implements AlignViewportI, */ private boolean selectionIsDefinedGroup = false; - @Override public boolean isSelectionDefinedGroup() {