import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
{
setAlignment(al);
- posProps.setHiddenColumns(hiddenColumns);
- /*if (hiddenColumns != null)
+ if (hiddenColumns != null)
{
colSel = hiddenColumns;
- }*/
+ }
init();
}
Cache.log.debug("Setting viewport's view id : " + viewId);
}
setAlignment(al);
- posProps.setHiddenColumns(hiddenColumns);
- /*if (hiddenColumns != null)
+ if (hiddenColumns != null)
{
colSel = hiddenColumns;
- }*/
+ }
init();
}
void init()
{
-
- /*setStartRes(0);
- setEndRes(alignment.getWidth() - 1);
- setStartSeq(0);
- setEndSeq(alignment.getHeight() - 1);*/
+ ranges = new ViewportRanges(this.alignment);
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
{
residueShading.setConsensus(hconsensus);
}
-
- posProps = new ViewportPositionProps(this.alignment, this.viewStyle);
}
/**
{
end = alignment.getWidth();
}
- viscontigs = posProps.getColumnSelection()
- .getVisibleContigs(start, end);
- // viscontigs = colSel.getVisibleContigs(start, end);
+ viscontigs = colSel.getVisibleContigs(start, end);
return viscontigs;
}
}
}
- setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight());
firePropertyChange("alignment", null, getAlignment().getSequences());
}