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;
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)
schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
ResidueColourScheme.NONE);
}
- ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(this, alignment, schemeName);
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+ alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
{
return validCharWidth;
}
+
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
// calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
if (needsUpdate)
{
- Cache.log.debug("trigger update for " + calcId);
+ Console.debug("trigger update for " + calcId);
}
}
@Override
public void run()
{
- addDataToAlignment(al);
+ addDataToAlignment(al);
}
}).setResponseHandler(SPLIT_FRAME, new Runnable()
{
try
{
- newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
}
/**
- * Applies the supplied feature settings descriptor to currently known features.
- * This supports an 'initial configuration' of feature colouring based on a
- * preset or user favourite. This may then be modified in the usual way using
- * the Feature Settings dialogue.
+ * Applies the supplied feature settings descriptor to currently known
+ * features. This supports an 'initial configuration' of feature colouring
+ * based on a preset or user favourite. This may then be modified in the usual
+ * way using the Feature Settings dialogue.
*
* @param featureSettings
*/
/**
* when mergeOnly is set, then group and feature visibility or feature colours
* are not modified for features and groups already known to the feature
- * renderer. Feature ordering is always adjusted, and transparency is always set
- * regardless.
+ * renderer. Feature ordering is always adjusted, and transparency is always
+ * set regardless.
*
* @param featureSettings
* @param mergeOnly
{
return;
}
-
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
List<String> origRenderOrder = new ArrayList(),
origGroups = new ArrayList();
- // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+ // preserve original render order - allows differentiation between user
+ // configured colours and autogenerated ones
origRenderOrder.addAll(fr.getRenderOrder());
origGroups.addAll(fr.getFeatureGroups());
&& origColour.getColour().equals(
ColorUtils.createColourFromName(type)))))
{
- // if we are merging, only update if there wasn't already a colour defined for
+ // if we are merging, only update if there wasn't already a colour
+ // defined for
// this type
if (preferredColour != null)
{
{
if (!mergeOnly || !origGroups.contains(group))
{
- // when merging, display groups only if the aren't already marked as not visible
+ // when merging, display groups only if the aren't already marked as not
+ // visible
fr.setGroupVisibility(group,
featureSettings.isGroupDisplayed(group));
}
fr.orderFeatures(featureSettings);
}
fr.setTransparency(featureSettings.getTransparency());
+
fr.notifyFeaturesChanged();
}