import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
-import java.util.Iterator;
import java.util.List;
import javax.swing.JInternalFrame;
boolean antiAlias = false;
- private Rectangle explodedGeometry;
+ private Rectangle explodedGeometry = null;
- private String viewName;
+ private String viewName = null;
/*
* Flag set true on the view that should 'gather' multiple views of the same
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
init();
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
if (hiddenColumns != null)
*/
private void applyViewProperties()
{
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+ antiAlias = Cache.getDefault("ANTI_ALIAS", true);
viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
}
/**
- * returns the visible column regions of the alignment
- *
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the selected
- * area
- * @return
- */
- public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
- {
- int start = 0;
- int end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- end = alignment.getWidth();
- }
- return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
- false));
- }
-
- /**
* get hash of undo and redo list for the alignment
*
* @return long[] { historyList.hashCode, redoList.hashCode };
// calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
if (needsUpdate)
{
- Cache.log.debug("trigger update for " + calcId);
+ Console.debug("trigger update for " + calcId);
}
}
try
{
newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
if (ap != null)
{
// modify GUI elements to reflect geometry change
- Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
- .getPreferredSize();
+ Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
idw.width = i;
- getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
}
}
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
- List<String> origRenderOrder = new ArrayList(),
- origGroups = new ArrayList();
+ List<String> origRenderOrder = new ArrayList<>();
+ List<String> origGroups = new ArrayList<>();
// preserve original render order - allows differentiation between user configured colours and autogenerated ones
origRenderOrder.addAll(fr.getRenderOrder());
origGroups.addAll(fr.getFeatureGroups());
if (!mergeOnly)
{
// only clear displayed features if we are mergeing
- displayed.clear();
+ // displayed.clear();
}
// TODO this clears displayed.featuresRegistered - do we care?
//
{
displayed.setVisible(type);
}
+ else if (featureSettings.isFeatureHidden(type))
+ {
+ displayed.setHidden(type);
+ }
}
}
fr.orderFeatures(featureSettings);
}
fr.setTransparency(featureSettings.getTransparency());
+
+ fr.notifyFeaturesChanged();
}
public String getViewName()