*/
package jalview.appletgui;
+import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.MouseMotionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.util.Arrays;
import java.util.Enumeration;
-import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
public class FeatureSettings extends Panel implements ItemListener,
transparency = new Scrollbar(Scrollbar.HORIZONTAL,
100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
- if (fr.isTransparencyAvailable())
- {
- transparency.addAdjustmentListener(this);
- }
- else
- {
- transparency.setEnabled(false);
- }
+ transparency.addAdjustmentListener(this);
java.net.URL url = getClass().getResource("/images/link.gif");
if (url != null)
Panel tPanel = new Panel(new BorderLayout());
- if (fr.isTransparencyAvailable())
- {
- tPanel.add(transparency, BorderLayout.CENTER);
- tPanel.add(new Label("Transparency"), BorderLayout.EAST);
- }
- else
- {
- tPanel.add(
- new Label("Transparency not available in this web browser"),
- BorderLayout.CENTER);
- }
+ tPanel.add(transparency, BorderLayout.CENTER);
+ tPanel.add(new Label("Transparency"), BorderLayout.EAST);
lowerPanel.add(tPanel, BorderLayout.SOUTH);
60);
}
- protected void popupSort(final MyCheckbox check, final Hashtable minmax,
- int x, int y)
+ protected void popupSort(final MyCheckbox check,
+ final Map<String, float[][]> minmax, int x, int y)
{
final String type = check.type;
- final Object typeCol = fr.getFeatureStyle(type);
- java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
+ final FeatureColourI typeCol = fr.getFeatureStyle(type);
+ PopupMenu men = new PopupMenu(MessageManager.formatMessage(
"label.settings_for_type", new String[] { type }));
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
@Override
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc
- .sortAlignmentByFeatureScore(new String[] { type });
+ me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
+ .asList(new String[] { type }));
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc
- .sortAlignmentByFeatureDensity(new String[] { type });
+ me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
+ .asList(new String[] { type }));
}
});
men.add(dens);
+
if (minmax != null)
{
- final Object typeMinMax = minmax.get(type);
+ final float[][] typeMinMax = minmax.get(type);
/*
* final java.awt.CheckboxMenuItem chb = new
* java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
*
* }); men.add(chb);
*/
- if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+ if (typeMinMax != null && typeMinMax[0] != null)
{
// graduated colourschemes for those where minmax exists for the
// positional features
MenuItem mxcol = new MenuItem(
- (typeCol instanceof Color) ? "Graduated Colour"
+ (typeCol.isSimpleColour()) ? "Graduated Colour"
: "Single Colour");
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- if (typeCol instanceof Color)
+ if (typeCol.isSimpleColour())
{
new FeatureColourChooser(me, type);
// write back the current colour object to update the table
}
else
{
- new UserDefinedColours(me, check.type,
- ((GraduatedColor) typeCol));
+ new UserDefinedColours(me, check.type, typeCol);
}
}
});
}
}
+
+ MenuItem selectContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_containing"));
+ selectContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+ false, type);
+ }
+ });
+ men.add(selectContaining);
+
+ MenuItem selectNotContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_not_containing"));
+ selectNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+ false, type);
+ }
+ });
+ men.add(selectNotContaining);
+
+ MenuItem hideContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_containing"));
+ hideContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, true);
+ }
+ });
+ men.add(hideContaining);
+
+ MenuItem hideNotContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_not_containing"));
+ hideNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, false);
+ }
+ });
+ men.add(hideNotContaining);
+
this.featurePanel.add(men);
men.show(this.featurePanel, x, y);
}
{
SequenceFeature[] tmpfeatures;
String group = null, type;
- Vector visibleChecks = new Vector();
+ Vector<String> visibleChecks = new Vector<String>();
AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
// now add checkboxes which should be visible,
// if they have not already been added
- Enumeration en = visibleChecks.elements();
+ Enumeration<String> en = visibleChecks.elements();
while (en.hasMoreElements())
{
}
}
- public void setUserColour(String feature, Object originalColour)
+ public void setUserColour(String feature, FeatureColourI originalColour)
{
- if (originalColour instanceof Color
- || originalColour instanceof GraduatedColor)
- {
- fr.setColour(feature, originalColour);
- }
- else
- {
- throw new Error(
- MessageManager
- .getString("error.implementation_error_unsupported_feature_colour_object"));
- }
+ fr.setColour(feature, originalColour);
refreshTable();
}
if (evt.getClickCount() > 1)
{
- Object fcol = fr.getFeatureStyle(check.type);
- if (fcol instanceof Color)
+ FeatureColourI fcol = fr.getFeatureStyle(check.type);
+ if (fcol.isSimpleColour())
{
- new UserDefinedColours(this, check.type, (Color) fcol);
+ new UserDefinedColours(this, check.type, fcol.getColour());
}
else
{
boolean hasLink;
- GraduatedColor gcol;
-
- Color col;
+ FeatureColourI col;
- public void updateColor(Object newcol)
+ public void updateColor(FeatureColourI newcol)
{
- if (newcol instanceof Color)
+ col = newcol;
+ if (col.isSimpleColour())
{
- col = (Color) newcol;
- gcol = null;
- }
- else if (newcol instanceof GraduatedColor)
- {
- gcol = (GraduatedColor) newcol;
- col = null;
- }
- else
- {
- throw new Error(
- MessageManager
- .getString("error.invalid_colour_for_mycheckbox"));
- }
- if (col != null)
- {
- setBackground(col);
+ setBackground(col.getColour());
}
else
{
String vlabel = type;
- if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (col.isAboveThreshold())
+ {
+ vlabel += " (>)";
+ }
+ else if (col.isBelowThreshold())
{
- vlabel += " "
- + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
- : "(<)");
+ vlabel += " (<)";
}
- if (gcol.isColourByLabel())
+ if (col.isColourByLabel())
{
setBackground(Color.white);
vlabel += " (by Label)";
}
else
{
- setBackground(gcol.getMinColor());
+ setBackground(col.getMinColour());
}
this.setLabel(vlabel);
}
}
public MyCheckbox(String type, boolean selected, boolean b,
- Object featureStyle)
+ FeatureColourI featureStyle)
{
this(type, selected, b);
updateColor(featureStyle);
public void paint(Graphics g)
{
Dimension d = getSize();
- if (gcol != null)
+ if (col != null)
{
- if (gcol.isColourByLabel())
+ if (col.isColourByLabel())
{
g.setColor(Color.white);
g.fillRect(d.width / 2, 0, d.width / 2, d.height);
*/
}
- else
+ else if (col.isGraduatedColour())
{
- Color maxCol = gcol.getMaxColor();
+ Color maxCol = col.getMaxColour();
g.setColor(maxCol);
g.fillRect(d.width / 2, 0, d.width / 2, d.height);
}
}
+ /**
+ * Hide columns containing (or not containing) a given feature type
+ *
+ * @param type
+ * @param columnsContaining
+ */
+ void hideFeatureColumns(final String type, boolean columnsContaining)
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+ false, false, type))
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(
+ !columnsContaining, false, false, type))
+ {
+ ap.alignFrame.viewport.hideSelectedColumns();
+ }
+ }
+ }
+
@Override
public void mousePressed(MouseEvent e)
{
+ // TODO Auto-generated method stub
+
}
}
git://source.jalview.org / jalview.git / blobdiff