*/
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceGroup;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Checkbox;
import java.awt.CheckboxGroup;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
/**
* A panel that allows the user to select which sequence-associated annotation
* rows to show or hide.
private void showFrame()
{
frame = new JInternalFrame();
+ frame.setFrameIcon(WindowIcons.annotationIcon);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
-import jalview.gui.JalviewColourChooser.ColourChooserListener;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
}
}
frame = new JInternalFrame();
+ frame.setFrameIcon(WindowIcons.annotationIcon);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.io.cache.JvCacheableInputBox;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
import javax.swing.JRadioButton;
import javax.swing.border.TitledBorder;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.io.cache.JvCacheableInputBox;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
{
super(av, ap);
frame = new JInternalFrame();
+ frame.setFrameIcon(WindowIcons.annotationIcon);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
*/
package jalview.gui;
-import java.util.Locale;
-
-import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AnnotationFile;
-import jalview.io.FeaturesFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.FileWriter;
import java.io.PrintWriter;
+import java.util.Locale;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JRadioButton;
import javax.swing.SwingConstants;
+import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
+
/**
*
* GUI dialog for exporting features or alignment annotations depending upon
}
frame = new JInternalFrame();
+ frame.setFrameIcon(WindowIcons.annotationIcon);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Dimension preferredSize = frame.getPreferredSize();
*/
package jalview.gui;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.RnaViewerModel;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.ext.varna.RnaModel;
-import jalview.structure.SecondaryStructureListener;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.ShiftList;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.util.Collection;
import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.RnaModel;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
public class AppVarna extends JInternalFrame
implements SelectionListener, SecondaryStructureListener,
*/
protected AppVarna(AlignmentPanel ap)
{
+ this.setFrameIcon(null);
this.ap = ap;
this.viewId = System.currentTimeMillis() + "." + this.hashCode();
vab = new AppVarnaBinding();
*/
package jalview.gui;
-import jalview.analysis.TreeBuilder;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.analysis.scoremodels.SimilarityParams;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceGroup;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
/**
* A dialog where a user can choose and action Tree or PCA calculation options
*/
{
setLayout(new BorderLayout());
frame = new JInternalFrame();
+ frame.setFrameIcon(WindowIcons.treeIcon);
frame.setContentPane(this);
this.setBackground(Color.white);
frame.addFocusListener(new FocusListener()
*/
protected void init()
{
+ setFrameIcon(WindowIcons.splitIcon);
getTopFrame().setSplitFrame(this);
getBottomFrame().setSplitFrame(this);
getTopFrame().setVisible(true);
public StructureViewerBase()
{
super();
+ setFrameIcon(WindowIcons.structureIcon);
}
/**
protected static final ImageIcon structureIcon = new ImageIcon(
WindowIcons.class
.getResource("/images/windowIcons/structureIcon.png"));
+
+ protected static final ImageIcon splitIcon = new ImageIcon(
+ WindowIcons.class
+ .getResource("/images/windowIcons/splitIcon.png"));
}