*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemes.FeatureColour;
+import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.QuickSort;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import java.util.Vector;
table.setDefaultEditor(Color.class, new ColorEditor(this));
- table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this));
- table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer());
+ table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+ table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
table.addMouseMotionListener(new MouseMotionAdapter()
{
+ @Override
public void mouseDragged(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (!fs.resettingTable && !fs.handlingUpdate)
frame = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
+ if (Platform.isAMac())
{
Desktop.addInternalFrame(frame,
MessageManager.getString("label.sequence_feature_settings"),
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
- protected void popupSort(final int selectedRow, final String type,
- final Object typeCol, final Hashtable minmax, int x, int y)
+ protected void popupSort(final int row, final String type,
+ final Object typeCol, final Map<String, float[][]> minmax, int x,
+ int y)
{
+ final FeatureColourI featureColour = (FeatureColourI) typeCol;
+
JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
"label.settings_for_param", new String[] { type }));
JMenuItem scr = new JMenuItem(
scr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
dens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
men.add(dens);
if (minmax != null)
{
- final Object typeMinMax = minmax.get(type);
+ final float[][] typeMinMax = minmax.get(type);
/*
* final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
* this is broken at the moment and isn't that useful anyway!
*
* men.add(chb);
*/
- if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+ if (typeMinMax != null && typeMinMax[0] != null)
{
// if (table.getValueAt(row, column));
// graduated colourschemes for those where minmax exists for the
// positional features
final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
"Graduated Colour");
- mxcol.setSelected(!(typeCol instanceof Color));
+ mxcol.setSelected(!featureColour.isSimpleColour());
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
{
JColorChooser colorChooser;
+ @Override
public void actionPerformed(ActionEvent e)
{
if (e.getSource() == mxcol)
{
- if (typeCol instanceof Color)
+ if (featureColour.isSimpleColour())
{
FeatureColourChooser fc = new FeatureColourChooser(me.fr,
type);
"Select new Colour", true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
- colorChooser.setColor(((GraduatedColor) typeCol)
- .getMaxColor());
+ colorChooser.setColor(featureColour.getMaxColour());
dialog.setVisible(true);
}
}
{
FeatureColourChooser fc = (FeatureColourChooser) e
.getSource();
- table.setValueAt(fc.getLastColour(), selectedRow, 1);
+ table.setValueAt(fc.getLastColour(), row, 1);
table.validate();
}
else
{
// probably the color chooser!
- table.setValueAt(colorChooser.getColor(), selectedRow, 1);
+ table.setValueAt(colorChooser.getColor(), row, 1);
table.validate();
me.updateFeatureRenderer(
((FeatureTableModel) table.getModel()).getData(),
/**
* contains a float[3] for each feature type string. created by setTableData
*/
- Hashtable typeWidth = null;
+ Map<String, float[]> typeWidth = null;
@Override
synchronized public void discoverAllFeatureData()
{
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ Vector<String> allFeatures = new Vector<String>();
+ Vector<String> allGroups = new Vector<String>();
SequenceFeature[] tmpfeatures;
String group;
for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
check.setFont(new Font("Serif", Font.BOLD, 12));
check.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
fr.setGroupVisibility(check.getText(), check.isSelected());
return;
}
resettingTable = true;
- typeWidth = new Hashtable();
+ typeWidth = new Hashtable<String, float[]>();
// TODO: change avWidth calculation to 'per-sequence' average and use long
// rather than float
float[] avWidth = null;
SequenceFeature[] tmpfeatures;
String group = null, type;
- Vector visibleChecks = new Vector();
+ Vector<String> visibleChecks = new Vector<String>();
// Find out which features should be visible depending on which groups
// are selected / deselected
}
else
{
- avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
+ avWidth = typeWidth.get(tmpfeatures[index].getType());
}
avWidth[0]++;
if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
InputStreamReader in = new InputStreamReader(new FileInputStream(
file), "UTF-8");
- jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = jucs.unmarshal(in);
+ JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
Cache.log.warn("Couldn't parse out graduated feature color.",
e);
}
- GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+ FeatureColourI gcol = new FeatureColour(mincol, maxcol,
newcol.getMin(), newcol.getMax());
if (newcol.hasAutoScale())
{
}
if (newcol.hasThreshold())
{
- gcol.setThresh(newcol.getThreshold());
- gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
+ gcol.setThreshold(newcol.getThreshold());
}
if (newcol.getThreshType().length() > 0)
{
String ttyp = newcol.getThreshType();
- if (ttyp.equalsIgnoreCase("NONE"))
- {
- gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
- }
if (ttyp.equalsIgnoreCase("ABOVE"))
{
- gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ gcol.setAboveThreshold(true);
}
if (ttyp.equalsIgnoreCase("BELOW"))
{
- gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ gcol.setBelowThreshold(true);
}
}
fr.setColour(name = newcol.getName(), gcol);
}
else
{
- fr.setColour(name = jucs.getColour(i).getName(), new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ Color color = new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16));
+ fr.setColour(name = jucs.getColour(i).getName(),
+ new FeatureColour(color));
}
fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
}
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
- Set fr_colours = fr.getAllFeatureColours();
- Iterator e = fr_colours.iterator();
+ Set<String> fr_colours = fr.getAllFeatureColours();
+ Iterator<String> e = fr_colours.iterator();
float[] sortOrder = new float[fr_colours.size()];
String[] sortTypes = new String[fr_colours.size()];
int i = 0;
while (e.hasNext())
{
- sortTypes[i] = e.next().toString();
+ sortTypes[i] = e.next();
sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
- jalview.util.QuickSort.sort(sortOrder, sortTypes);
+ QuickSort.sort(sortOrder, sortTypes);
sortOrder = null;
- Object fcol;
- GraduatedColor gcol;
for (i = 0; i < sortTypes.length; i++)
{
jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(sortTypes[i]);
- col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
- .getName())));
- fcol = fr.getFeatureStyle(sortTypes[i]);
- if (fcol instanceof GraduatedColor)
+ FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
+ if (fcol.isSimpleColour())
{
- gcol = (GraduatedColor) fcol;
- col.setMin(gcol.getMin());
- col.setMax(gcol.getMax());
- col.setMinRGB(jalview.util.Format.getHexString(gcol
- .getMinColor()));
- col.setAutoScale(gcol.isAutoScale());
- col.setThreshold(gcol.getThresh());
- col.setColourByLabel(gcol.isColourByLabel());
- switch (gcol.getThreshType())
- {
- case AnnotationColourGradient.NO_THRESHOLD:
- col.setThreshType("NONE");
- break;
- case AnnotationColourGradient.ABOVE_THRESHOLD:
- col.setThreshType("ABOVE");
- break;
- case AnnotationColourGradient.BELOW_THRESHOLD:
- col.setThreshType("BELOW");
- break;
- }
+ col.setRGB(Format.getHexString(fcol.getColour()));
+ }
+ else
+ {
+ col.setRGB(Format.getHexString(fcol.getMaxColour()));
+ col.setMin(fcol.getMin());
+ col.setMax(fcol.getMax());
+ col.setMinRGB(jalview.util.Format.getHexString(fcol
+ .getMinColour()));
+ col.setAutoScale(fcol.isAutoScaled());
+ col.setThreshold(fcol.getThreshold());
+ col.setColourByLabel(fcol.isColourByLabel());
+ col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol
+ .isBelowThreshold() ? "BELOW" : "NONE"));
}
ucs.addColour(col);
}
int num = 0;
for (int i = 0; i < data.length; i++)
{
- awidth = (float[]) typeWidth.get(data[i][0]);
+ awidth = typeWidth.get(data[i][0]);
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
invert.setText(MessageManager.getString("label.invert_selection"));
invert.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
invertSelection();
optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
optimizeOrder.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
orderByAvWidth();
.setText(MessageManager.getString("label.seq_sort_by_score"));
sortByScore.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
af.avc.sortAlignmentByFeatureScore(null);
.getString("label.sequence_sort_by_density"));
sortByDens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
af.avc.sortAlignmentByFeatureDensity(null);
help.setText(MessageManager.getString("action.help"));
help.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
try
help.setText(MessageManager.getString("action.help"));
help.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
try
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fr.setTransparency(originalTransparency);
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close();
loadColours.setText(MessageManager.getString("label.load_colours"));
loadColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
load();
saveColours.setText(MessageManager.getString("label.save_colours"));
saveColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
save();
});
transparency.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
fetchDAS.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fetchDAS_actionPerformed(e);
saveDAS.setText(MessageManager.getString("action.save_as_default"));
saveDAS.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
saveDAS_actionPerformed(e);
cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
cancelDAS.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancelDAS_actionPerformed(e);
fetchDAS.setEnabled(false);
cancelDAS.setEnabled(true);
dassourceBrowser.setGuiEnabled(false);
- Vector selectedSources = dassourceBrowser.getSelectedSources();
+ Vector<jalviewSourceI> selectedSources = dassourceBrowser
+ .getSelectedSources();
doDasFeatureFetch(selectedSources, true, true);
}
* Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
- public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
+ public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
{
return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
}
*
* @return vector of selected das source nicknames
*/
- public Vector getSelectedSources()
+ public Vector<jalviewSourceI> getSelectedSources()
{
return dassourceBrowser.getSelectedSources();
}
* if true then runs in same thread, otherwise passes to the Swing
* executor
*/
- public void fetchDasFeatures(Vector sources, boolean block)
+ public void fetchDasFeatures(Vector<String> sources, boolean block)
{
initDasSources();
List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
Runnable fetcher = new Runnable()
{
+ @Override
public void run()
{
doDasFeatureFetch(dassources, true, false);
this.data = data;
}
+ @Override
public int getColumnCount()
{
return columnNames.length;
return data[row];
}
+ @Override
public int getRowCount()
{
return data.length;
}
+ @Override
public String getColumnName(int col)
{
return columnNames[col];
}
+ @Override
public Object getValueAt(int row, int col)
{
return data[row][col];
}
+ @Override
public Class getColumnClass(int c)
{
return getValueAt(0, c).getClass();
}
+ @Override
public boolean isCellEditable(int row, int col)
{
return col == 0 ? false : true;
}
+ @Override
public void setValueAt(Object value, int row, int col)
{
data[row][col] = value;
setVerticalTextPosition(SwingConstants.CENTER);
}
- public Component getTableCellRendererComponent(JTable table,
+ @Override
+ public Component getTableCellRendererComponent(JTable tbl,
Object color, boolean isSelected, boolean hasFocus, int row,
int column)
{
+ FeatureColourI cellColour = (FeatureColourI) color;
// JLabel comp = new JLabel();
// comp.
setOpaque(true);
// setBounds(getBounds());
Color newColor;
setToolTipText(baseTT);
- setBackground(table.getBackground());
- if (color instanceof GraduatedColor)
+ setBackground(tbl.getBackground());
+ if (!cellColour.isSimpleColour())
{
- Rectangle cr = table.getCellRect(row, column, false);
- FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color,
+ Rectangle cr = tbl.getCellRect(row, column, false);
+ FeatureSettings.renderGraduatedColor(this, cellColour,
(int) cr.getWidth(), (int) cr.getHeight());
}
{
this.setText("");
this.setIcon(null);
- newColor = (Color) color;
- // comp.
+ newColor = cellColour.getColour();
setBackground(newColor);
- // comp.setToolTipText("RGB value: " + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue());
}
if (isSelected)
{
if (selectedBorder == null)
{
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getSelectionBackground());
+ tbl.getSelectionBackground());
}
- // comp.
setBorder(selectedBorder);
}
else
if (unselectedBorder == null)
{
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getBackground());
+ tbl.getBackground());
}
- // comp.
setBorder(unselectedBorder);
}
* @param comp
* @param gcol
*/
- public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol)
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
{
int w = comp.getWidth(), h = comp.getHeight();
if (w < 20)
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol,
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
int w, int h)
{
boolean thr = false;
String tt = "";
String tx = "";
- if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD)
+ if (gcol.isAboveThreshold())
{
thr = true;
tx += ">";
- tt += "Thresholded (Above " + gcol.getThresh() + ") ";
+ tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
}
- if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+ if (gcol.isBelowThreshold())
{
thr = true;
tx += "<";
- tt += "Thresholded (Below " + gcol.getThresh() + ") ";
+ tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
}
if (gcol.isColourByLabel())
{
}
else
{
- Color newColor = gcol.getMaxColor();
+ Color newColor = gcol.getMaxColour();
comp.setBackground(newColor);
// System.err.println("Width is " + w / 2);
Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
class FeatureIcon implements Icon
{
- GraduatedColor gcol;
+ FeatureColourI gcol;
Color backg;
Color mpcolour = Color.white;
- FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace)
+ FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
{
gcol = gfc;
backg = bg;
}
}
+ @Override
public int getIconWidth()
{
return width;
}
+ @Override
public int getIconHeight()
{
return height;
}
+ @Override
public void paintIcon(Component c, Graphics g, int x, int y)
{
g.setColor(backg);
g.fillRect(0, 0, width, height);
// need an icon here.
- g.setColor(gcol.getMaxColor());
+ g.setColor(gcol.getMaxColour());
g.setFont(new Font("Verdana", Font.PLAIN, 9));
}
else
{
- Color minCol = gcol.getMinColor();
+ Color minCol = gcol.getMinColour();
g.setColor(minCol);
g.fillRect(0, 0, s1, height);
if (midspace)
g.setColor(Color.white);
g.fillRect(s1, 0, e1 - s1, height);
}
- g.setColor(gcol.getMaxColor());
+ g.setColor(gcol.getMaxColour());
g.fillRect(0, e1, width - e1, height);
}
}
{
FeatureSettings me;
- GraduatedColor currentGColor;
+ FeatureColourI currentColor;
FeatureColourChooser chooser;
String type;
- Color currentColor;
-
JButton button;
JColorChooser colorChooser;
/**
* Handles events from the editor button and from the dialog's OK button.
*/
+ @Override
public void actionPerformed(ActionEvent e)
{
{
// The user has clicked the cell, so
// bring up the dialog.
- if (currentColor != null)
+ if (currentColor.isSimpleColour())
{
// bring up simple color chooser
- button.setBackground(currentColor);
- colorChooser.setColor(currentColor);
+ button.setBackground(currentColor.getColour());
+ colorChooser.setColor(currentColor.getColour());
dialog.setVisible(true);
}
else
}
else
{ // User pressed dialog's "OK" button.
- if (currentColor != null)
+ if (currentColor.isSimpleColour())
{
- currentColor = colorChooser.getColor();
+ currentColor = new FeatureColour(colorChooser.getColor());
}
else
{
- // class cast exceptions may be raised if the chooser created on a
- // non-graduated color
- currentGColor = (GraduatedColor) chooser.getLastColour();
+ currentColor = chooser.getLastColour();
}
me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
fireEditingStopped();
}
// Implement the one CellEditor method that AbstractCellEditor doesn't.
+ @Override
public Object getCellEditorValue()
{
- if (currentColor == null)
- {
- return currentGColor;
- }
return currentColor;
}
// Implement the one method defined by TableCellEditor.
+ @Override
public Component getTableCellEditorComponent(JTable table, Object value,
boolean isSelected, int row, int column)
{
- currentGColor = null;
- currentColor = null;
+ currentColor = (FeatureColourI) value;
this.selectedRow = row;
type = me.table.getValueAt(row, 0).toString();
button.setOpaque(true);
button.setBackground(me.getBackground());
- if (value instanceof GraduatedColor)
+ if (!currentColor.isSimpleColour())
{
- currentGColor = (GraduatedColor) value;
JLabel btn = new JLabel();
btn.setSize(button.getSize());
- FeatureSettings.renderGraduatedColor(btn, currentGColor);
+ FeatureSettings.renderGraduatedColor(btn, currentColor);
button.setBackground(btn.getBackground());
button.setIcon(btn.getIcon());
button.setText(btn.getText());
{
button.setText("");
button.setIcon(null);
- currentColor = (Color) value;
- button.setBackground(currentColor);
+ button.setBackground(currentColor.getColour());
}
return button;
}
git://source.jalview.org / jalview.git / blobdiff