import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.ProfileI;
-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;
protected boolean ignoreGapsInConsensusCalculation = false;
- protected ColourSchemeI globalColourScheme = null;
+ protected ResidueShaderI residueShading;
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
// 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)
{
- 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.setConservationApplied(getConservationSelected());
- 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
+ /*
+ * retain any colour thresholds per group while
+ * changing choice of colour scheme (JAL-2386)
+ */
+ sg.setColourScheme(cs);
+ if (cs != null)
{
- sg.cs.setThreshold(0, isIgnoreGapsConsensus());
- }
-
- if (getConservationSelected())
- {
- 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);
}
}
}
@Override
public ColourSchemeI getGlobalColourScheme()
{
- return globalColourScheme;
+ return residueShading == null ? null : residueShading
+ .getColourScheme();
+ }
+
+ @Override
+ public ResidueShaderI getResidueShading()
+ {
+ return residueShading;
}
protected AlignmentAnnotation consensus;
/**
* results of alignment consensus analysis for visible portion of view
*/
- protected ProfileI[] hconsensus = null;
+ protected ProfilesI hconsensus = null;
/**
* results of cDNA complement consensus visible portion of view
}
@Override
- public void setSequenceConsensusHash(ProfileI[] hconsensus)
+ public void setSequenceConsensusHash(ProfilesI hconsensus)
{
this.hconsensus = hconsensus;
}
}
@Override
- public ProfileI[] getSequenceConsensusHash()
+ public ProfilesI getSequenceConsensusHash()
{
return hconsensus;
}
hconsensus = null;
hcomplementConsensus = null;
// colour scheme may hold reference to consensus
- globalColourScheme = null;
+ residueShading = null;
// TODO remove listeners from changeSupport?
changeSupport = null;
setAlignment(null);
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
+ if (sg != null)
+ {
+ sg.setContext(alignment);
+ }
}
public void setHiddenColumns(ColumnSelection colsel)
if (ap != null)
{
updateConsensus(ap);
- if (globalColourScheme != null)
+ if (residueShading != null)
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ residueShading.setThreshold(residueShading.getThreshold(),
ignoreGapsInConsensusCalculation);
}
}
selectionGroup.setEndRes(alWidth - 1);
}
- resetAllColourSchemes();
+ updateAllColourSchemes();
calculator.restartWorkers();
// alignment.adjustSequenceAnnotations();
}
/**
* 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",
+ rs.setConservation(Conservation.calculateConservation("All",
alignment.getSequences(), 0, alignment.getWidth(), false,
getConsPercGaps(), false));
}
* 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())
*/
private boolean selectionIsDefinedGroup = false;
+
@Override
public boolean isSelectionDefinedGroup()
{
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff