X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=544835da73b0517abf27e36e20968242a9b29b61;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=bd55668e752504025d0984783cbb370e84c8b2d7;hpb=47abd39554b389bbd420367a3291872e7b098727;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index bd55668..544835d 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -36,15 +36,15 @@ 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.schemes.ResidueProperties; import jalview.structure.CommandListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; @@ -58,6 +58,7 @@ 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; @@ -596,7 +597,7 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean ignoreGapsInConsensusCalculation = false; - protected ColourSchemeI globalColourScheme = null; + protected ResidueShaderI globalColourScheme; @Override public void setGlobalColourScheme(ColourSchemeI cs) @@ -604,73 +605,54 @@ 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 (globalColourScheme == null) + { + globalColourScheme = new ResidueShader(viewStyle); + } + globalColourScheme.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 + // if (getConservationSelected() || getAbovePIDThreshold() + // || cs instanceof PIDColourScheme + // || cs instanceof Blosum62ColourScheme) + if (getConservationSelected()) { - cs.setThreshold(0, ignoreGapsInConsensusCalculation); + globalColourScheme.setConservation(hconservation); } - if (recalc) - { - cs.setConsensus(hconsensus); - cs.setConservation(hconservation); - } - cs.alignmentChanged(alignment, hiddenRepSequences); + globalColourScheme.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()) - { - sg.cs.setConservationApplied(true); - recalc = true; - } - else + /* + * retain any colour thresholds per group while + * changing choice of colour scheme (JAL-2386) + */ + sg.setColourScheme(cs); + if (cs != null) { - sg.cs.setConservation(null); - // sg.cs.setThreshold(0, getIgnoreGapsConsensus()); - } - if (recalc) - { - sg.recalcConservation(); - } - else - { - sg.cs.alignmentChanged(sg, hiddenRepSequences); + sg.getGroupColourScheme() + .alignmentChanged(sg, hiddenRepSequences); } } } @@ -679,6 +661,13 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { + return globalColourScheme == null ? null : globalColourScheme + .getColourScheme(); + } + + @Override + public ResidueShaderI getViewportColourScheme() + { return globalColourScheme; } @@ -699,7 +688,7 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * results of alignment consensus analysis for visible portion of view */ - protected Hashtable[] hconsensus = null; + protected ProfilesI hconsensus = null; /** * results of cDNA complement consensus visible portion of view @@ -733,7 +722,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public void setSequenceConsensusHash(Hashtable[] hconsensus) + public void setSequenceConsensusHash(ProfilesI hconsensus) { this.hconsensus = hconsensus; } @@ -745,7 +734,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public Hashtable[] getSequenceConsensusHash() + public ProfilesI getSequenceConsensusHash() { return hconsensus; } @@ -807,7 +796,8 @@ public abstract class AlignmentViewport implements AlignViewportI, public void updateConservation(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null + if (alignment.isNucleotide() + || (conservation == null && quality == null) || !autoCalculateConsensus) { return; @@ -913,6 +903,37 @@ public abstract class AlignmentViewport implements AlignViewportI, return false; } + public void setAlignment(AlignmentI align) + { + this.alignment = align; + } + + /** + * Clean up references when this viewport is closed + */ + @Override + public void dispose() + { + /* + * defensively null out references to large objects in case + * this object is not garbage collected (as if!) + */ + consensus = null; + complementConsensus = null; + strucConsensus = null; + conservation = null; + quality = null; + groupConsensus = null; + groupConservation = null; + hconsensus = null; + hcomplementConsensus = null; + // colour scheme may hold reference to consensus + globalColourScheme = null; + // TODO remove listeners from changeSupport? + changeSupport = null; + setAlignment(null); + } + @Override public boolean isClosed() { @@ -1107,6 +1128,13 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public boolean hasSelectedColumns() + { + ColumnSelection columnSelection = getColumnSelection(); + return columnSelection != null && columnSelection.hasSelectedColumns(); + } + + @Override public boolean hasHiddenColumns() { return colSel != null && colSel.hasHiddenColumns(); @@ -1233,10 +1261,9 @@ public abstract class AlignmentViewport implements AlignViewportI, return ignoreGapsInConsensusCalculation; } - // / property change stuff - + // property change stuff // JBPNote Prolly only need this in the applet version. - private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); protected boolean showConservation = true; @@ -1537,7 +1564,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public boolean isHiddenRepSequence(SequenceI seq) { return (hiddenRepSequences != null && hiddenRepSequences - .containsKey(seq)); + .containsKey(seq)); } /** @@ -1809,7 +1836,7 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.setEndRes(alWidth - 1); } - resetAllColourSchemes(); + updateAllColourSchemes(); calculator.restartWorkers(); // alignment.adjustSequenceAnnotations(); } @@ -1817,19 +1844,19 @@ 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 = globalColourScheme; + 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", - ResidueProperties.propHash, 3, alignment.getSequences(), 0, - alignment.getWidth(), false, getConsPercGaps(), false)); + rs.setConservation(Conservation.calculateConservation("All", + alignment.getSequences(), 0, alignment.getWidth(), false, + getConsPercGaps(), false)); } } @@ -2678,7 +2705,7 @@ 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()) @@ -2730,7 +2757,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } seqMappings = MappingUtils .findMappingsForSequenceAndOthers(sequence, mappings, - getCodingComplement().getAlignment()); + getCodingComplement().getAlignment().getSequences()); if (!seqMappings.isEmpty()) { break; @@ -2760,11 +2787,9 @@ public abstract class AlignmentViewport implements AlignViewportI, public void expandColSelection(SequenceGroup sg, boolean wholewidth) { int sgs, sge; - if (sg != null - && (sgs = sg.getStartRes()) >= 0 + if (sg != null && (sgs = sg.getStartRes()) >= 0 && sg.getStartRes() <= (sge = sg.getEndRes()) - && (colSel == null || colSel.getSelected() == null || colSel - .getSelected().size() == 0)) + && !this.hasSelectedColumns()) { if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) { @@ -2787,6 +2812,7 @@ public abstract class AlignmentViewport implements AlignViewportI, */ private boolean selectionIsDefinedGroup = false; + @Override public boolean isSelectionDefinedGroup() { @@ -2810,4 +2836,27 @@ 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; + } }