import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
String seqsetid)
{
this(al, hiddenColumns, seqsetid, null);
String seqsetid)
{
this(al, hiddenColumns, seqsetid, null);
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
}
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
}
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
- // fall back on this property for backwards compatibility
- propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ // only DEFAULT_COLOUR available in Jalview before 2.9
+ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
- if (propertyValue != null)
- {
- ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
- alignment, propertyValue);
- residueShading = new ResidueShader(colourScheme);
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+ alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- if (colourScheme instanceof UserColourScheme)
- {
- residueShading = new ResidueShader(
- UserDefinedColours.loadDefaultColours());
- residueShading.setThreshold(0, isIgnoreGapsConsensus());
- }
+ if (colourScheme instanceof UserColourScheme)
+ {
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
+ }
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(Desktop.instance).sendSelection(
new SequenceGroup(getSelectionGroup()),
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(Desktop.instance).sendSelection(
new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()),
+ this);
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();