import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourScheme;
+import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, CommandListener
+ SelectionSource
{
Font font;
*/
public AlignViewport(AlignmentI al)
{
- setAlignment(al);
+ super(al);
init();
}
public AlignViewport(AlignmentI al, String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
init();
+
}
/**
*/
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
{
- setAlignment(al);
+ super(al);
if (hiddenColumns != null)
{
colSel = hiddenColumns;
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
+
if (hiddenColumns != null)
{
colSel = hiddenColumns;
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
- String propertyValue = Cache.getProperty(colourProperty);
- if (propertyValue == null)
+ String schemeName = Cache.getProperty(colourProperty);
+ if (schemeName == null)
{
- // 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);
- globalColourScheme = new CollectionColourScheme(colourScheme);
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+ alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- if (colourScheme instanceof UserColourScheme)
- {
- globalColourScheme = new CollectionColourScheme(
- UserDefinedColours.loadDefaultColours());
- globalColourScheme.setThreshold(0, isIgnoreGapsConsensus());
- }
+ if (colourScheme instanceof UserColourScheme)
+ {
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
+ }
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
+ if (residueShading != null)
+ {
+ residueShading.setConsensus(hconsensus);
}
}
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
-
}
/**
}
}
- setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight());
firePropertyChange("alignment", null, getAlignment().getSequences());
}