*/
package jalview.appletgui;
-import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
import java.awt.Font;
import java.awt.FontMetrics;
-public class AlignViewport extends AlignmentViewport implements
- SelectionSource
+public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
{
boolean cursorMode = false;
boolean validCharWidth = true;
- TreeModel currentTree = null;
-
public jalview.bin.JalviewLite applet;
- boolean MAC = false;
-
private AnnotationColumnChooser annotationColumnSelectionState;
- @Override
- public void finalize()
- {
- applet = null;
- quality = null;
- alignment = null;
- colSel = null;
- }
-
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
{
try
{
- widthScale = new Float(param).floatValue();
+ widthScale = Float.valueOf(param).floatValue();
} catch (Exception e)
{
}
if (widthScale <= 1.0)
{
- System.err
- .println("Invalid alignment character width scaling factor ("
+ System.err.println(
+ "Invalid alignment character width scaling factor ("
+ widthScale + "). Ignoring.");
widthScale = 1;
}
if (JalviewLite.debug)
{
- System.err
- .println("Alignment character width scaling factor is now "
+ System.err.println(
+ "Alignment character width scaling factor is now "
+ widthScale);
}
}
{
try
{
- heightScale = new Float(param).floatValue();
+ heightScale = Float.valueOf(param).floatValue();
} catch (Exception e)
{
}
if (heightScale <= 1.0)
{
- System.err
- .println("Invalid alignment character height scaling factor ("
+ System.err.println(
+ "Invalid alignment character height scaling factor ("
+ heightScale + "). Ignoring.");
heightScale = 1;
}
if (JalviewLite.debug)
{
- System.err
- .println("Alignment character height scaling factor is now "
+ System.err.println(
+ "Alignment character height scaling factor is now "
+ heightScale);
}
}
}
setFont(font, true);
- MAC = new jalview.util.Platform().isAMac();
-
if (applet != null)
{
- setShowJVSuffix(applet.getDefaultParameter("showFullId",
- getShowJVSuffix()));
+ setShowJVSuffix(
+ applet.getDefaultParameter("showFullId", getShowJVSuffix()));
setShowAnnotation(applet.getDefaultParameter("showAnnotation",
isShowAnnotation()));
setShowUnconserved(applet.getDefaultParameter("showUnconserved",
getShowUnconserved()));
- setScaleProteinAsCdna(applet.getDefaultParameter(
- "scaleProteinAsCdna", isScaleProteinAsCdna()));
+ setScaleProteinAsCdna(applet.getDefaultParameter("scaleProteinAsCdna",
+ isScaleProteinAsCdna()));
String param = applet.getParameter("upperCase");
if (param != null)
if (applet != null)
{
- String colour = al.isNucleotide() ? applet
- .getParameter("defaultColourNuc") : applet
- .getParameter("defaultColourProt");
+ String colour = al.isNucleotide()
+ ? applet.getParameter("defaultColourNuc")
+ : applet.getParameter("defaultColourProt");
if (colour == null)
{
colour = applet.getParameter("defaultColour");
if (colour != null)
{
residueShading = new ResidueShader(
- ColourSchemeProperty.getColourScheme(alignment, colour));
+ ColourSchemeProperty.getColourScheme(this, alignment,
+ colour));
if (residueShading != null)
{
residueShading.setConsensus(hconsensus);
if (applet.getParameter("userDefinedColour") != null)
{
- residueShading = new ResidueShader(
- new UserColourScheme(
- applet.getParameter("userDefinedColour")));
+ residueShading = new ResidueShader(new UserColourScheme(
+ applet.getParameter("userDefinedColour")));
}
}
initAutoAnnotation();
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2);
- setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
+ setCharWidth(
+ (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
}
}
public void resetSeqLimits(int height)
{
- ranges.setEndSeq(height / getCharHeight());
- }
-
- public void setCurrentTree(TreeModel tree)
- {
- currentTree = tree;
- }
-
- public TreeModel getCurrentTree()
- {
- return currentTree;
+ ranges.setEndSeq(height / getCharHeight() - 1); // BH 2019.04.18
}
boolean centreColumnLabels;
}
/**
- * 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. NOT IMPLEMENTED FOR APPLET
*
* @param featureSettings
*/
// TODO implement for applet
}
+ /**
+ * Merges the supplied feature settings descriptor with existing feature styles.
+ * 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. NOT IMPLEMENTED FOR APPLET
+ *
+ * @param featureSettings
+ */
+ @Override
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ // TODO Auto-generated method stub
+
+ }
}