X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=47f7d9dbd62fd232cf72de86a2fa2a5b9f4fabc8;hb=80fbfc0050c934ccdab11ccbd5f87d517ff4c04a;hp=6ecfe991a1a87586ef9825684116cc7796506606;hpb=1c757dc1e6ee864277825c1ebd9c6a9fbe0da7b2;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 6ecfe99..47f7d9d 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -22,7 +22,6 @@ package jalview.viewmodel; 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 +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.structure.CommandListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; @@ -78,6 +78,8 @@ import java.util.Map; public abstract class AlignmentViewport implements AlignViewportI, CommandListener, VamsasSource { + protected ViewportPositionProps posProps; + 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) + if (getConservationSelected()) { - recalc = true; - cs.setThreshold(viewStyle.getThreshold(), - ignoreGapsInConsensusCalculation); + residueShading.setConservation(hconservation); } - else - { - cs.setThreshold(0, ignoreGapsInConsensusCalculation); - } - if (recalc) - { - cs.setConsensus(hconsensus); - cs.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()) - { - 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); } } } @@ -680,7 +660,14 @@ 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; @@ -700,7 +687,7 @@ 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 +721,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public void setSequenceConsensusHash(Profile[] hconsensus) + public void setSequenceConsensusHash(ProfilesI hconsensus) { this.hconsensus = hconsensus; } @@ -746,7 +733,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public Profile[] getSequenceConsensusHash() + public ProfilesI getSequenceConsensusHash() { return hconsensus; } @@ -939,7 +926,9 @@ public abstract class AlignmentViewport implements AlignViewportI, groupConservation = null; hconsensus = null; hcomplementConsensus = null; - // TODO removed listeners from changeSupport? + // colour scheme may hold reference to consensus + residueShading = null; + // TODO remove listeners from changeSupport? changeSupport = null; setAlignment(null); } @@ -1086,7 +1075,8 @@ 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 @@ -1096,6 +1086,10 @@ 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) @@ -1208,9 +1202,9 @@ 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); } } @@ -1293,14 +1287,13 @@ public abstract class AlignmentViewport implements AlignViewportI, */ private boolean followHighlight = true; - // TODO private with getters and setters? - public int startRes; + /*private int startRes; - public int endRes; + private int endRes; - public int startSeq; + private int startSeq; - public int endSeq; + private int endSeq;*/ /** * Property change listener for changes in alignment @@ -1574,7 +1567,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public boolean isHiddenRepSequence(SequenceI seq) { return (hiddenRepSequences != null && hiddenRepSequences - .containsKey(seq)); + .containsKey(seq)); } /** @@ -1846,7 +1839,7 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.setEndRes(alWidth - 1); } - resetAllColourSchemes(); + updateAllColourSchemes(); calculator.restartWorkers(); // alignment.adjustSequenceAnnotations(); } @@ -1854,17 +1847,17 @@ 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)); } @@ -2438,6 +2431,11 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setViewStyle(ViewStyleI settingsForView) { viewStyle = new ViewStyle(settingsForView); + if (residueShading != null) + { + residueShading.setConservationApplied(settingsForView + .isConservationColourSelected()); + } } @Override @@ -2648,63 +2646,55 @@ public abstract class AlignmentViewport implements AlignViewportI, this.followHighlight = b; } + @Override + public ViewportPositionProps getPosProps() + { + return posProps; + } + + @Override public int getStartRes() { - return startRes; + return posProps.getStartRes(); } @Override public int getEndRes() { - return endRes; + return posProps.getEndRes(); } + @Override public int getStartSeq() { - return startSeq; + return posProps.getStartSeq(); } public void setStartRes(int res) { - this.startRes = res; + posProps.setStartRes(res); + // this.startRes = res; } public void setStartSeq(int seq) { - this.startSeq = seq; + posProps.setStartSeq(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; + posProps.setEndRes(res); } public void setEndSeq(int seq) { - if (seq > alignment.getHeight()) - { - seq = alignment.getHeight(); - } - if (seq < 0) - { - seq = 0; - } - this.endSeq = seq; + posProps.setEndSeq(seq); } + @Override public int getEndSeq() { - return endSeq; + return posProps.getEndSeq(); } /** @@ -2715,7 +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()) @@ -2797,8 +2787,7 @@ 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()) && !this.hasSelectedColumns()) { @@ -2823,6 +2812,7 @@ public abstract class AlignmentViewport implements AlignViewportI, */ private boolean selectionIsDefinedGroup = false; + @Override public boolean isSelectionDefinedGroup() { @@ -2846,4 +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; + } }