import javax.swing.event.*;
import javax.swing.table.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.commands.OrderCommand;
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.schemes.GraduatedColor;
public class FeatureSettings extends JPanel
{
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
+ if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ {
+ popupSort((String) table.getValueAt(selectedRow, 0), fr.minmax,
+ evt.getX(), evt.getY());
+ }
}
});
{
fs.handlingUpdate = true;
fs.resetTable(null); // new groups may be added with new seuqence
- // feature types only
+ // feature types only
fs.handlingUpdate = false;
}
}
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
+ protected void popupSort(final String type, final Hashtable minmax,
+ int x, int y)
+ {
+ JPopupMenu men = new JPopupMenu("Settings for " + type);
+ JMenuItem scr = new JMenuItem("Sort by Score");
+ men.add(scr);
+ final FeatureSettings me = this;
+ scr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.sortByScore(new String[]
+ { type });
+ }
+
+ });
+ JMenuItem dens = new JMenuItem("Sort by Density");
+ dens.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.sortByDens(new String[]
+ { type });
+ }
+
+ });
+ men.add(dens);
+ if (minmax != null)
+ {
+ final Object typeMinMax = minmax.get(type);
+ final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height");
+ // this is broken at the moment
+ chb.setSelected(minmax.get(type) != null);
+ chb.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ chb.setState(chb.getState());
+ if (chb.getState())
+ {
+ minmax.put(type, null);
+ }
+ else
+ {
+ minmax.put(type, typeMinMax);
+ }
+ }
+
+ });
+ men.add(chb);
+ if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+ {
+ // graduated colourschemes for those where minmax exists for the positional features
+ JMenuItem mxcol = new JMenuItem("Min Max Colour");
+ men.add(mxcol);
+ mxcol.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new FeatureColourChooser(me, type);
+ }
+
+ });
+ }
+ }
+ men.show(table, x, y);
+ }
+
/**
* true when Feature Settings are updating from feature renderer
*/
{
if (!handlingUpdate)
fr.findAllFeatures(groupChanged != null); // prod to update
- // colourschemes. but don't
- // affect display
+ // colourschemes. but don't
+ // affect display
// First add the checks in the previous render order,
// in case the window has been closed and reopened
for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
- // weight - but have to make per
- // sequence, too (awidth[2])
+ // weight - but have to make per
+ // sequence, too (awidth[2])
// if (width[i]==1) // hack to distinguish single width sequences.
num++;
}
JButton optimizeOrder = new JButton();
+ JButton sortByScore = new JButton();
+
+ JButton sortByDens = new JButton();
+
JPanel transbuttons = new JPanel(new BorderLayout());
private void jbInit() throws Exception
orderByAvWidth();
}
});
+ sortByScore.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ sortByScore.setText("Seq sort by Score");
+ sortByScore.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortByScore(null);
+ }
+ });
+ sortByDens.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ sortByDens.setText("Seq Sort by density");
+ sortByDens.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortByDens(null);
+ }
+ });
cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
cancel.setText("Cancel");
cancel.addActionListener(new ActionListener()
buttonPanel.add(cancel);
buttonPanel.add(loadColours);
buttonPanel.add(saveColours);
+ buttonPanel.add(sortByScore);
+ buttonPanel.add(sortByDens);
bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
dasButtonPanel.add(fetchDAS);
settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
}
+ protected void sortByDens(String[] typ)
+ {
+ sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ protected void sortBy(String[] typ, String methodText, final String method)
+ {
+ if (typ == null)
+ {
+ typ = getDisplayedFeatureTypes();
+ }
+ String gps[] = null;
+ gps = getDisplayedFeatureGroups();
+ if (typ != null)
+ {
+ for (int i = 0; i < typ.length; i++)
+ {
+ System.err.println("Sorting on Types:" + typ[i]);
+ }
+ }
+ if (gps != null)
+ {
+
+ for (int i = 0; i < gps.length; i++)
+ {
+ System.err.println("Sorting on groups:" + gps[i]);
+ }
+ }
+ AlignmentPanel alignPanel = af.alignPanel;
+ AlignmentI al = alignPanel.av.getAlignment();
+
+ int start, stop;
+ SequenceGroup sg = alignPanel.av.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();
+ }
+ else
+ {
+ start = 0;
+ stop = al.getWidth();
+ }
+ SequenceI[] oldOrder = al.getSequencesArray();
+ AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+ af.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av
+ .getAlignment()));
+ alignPanel.paintAlignment(true);
+
+ }
+
+ protected void sortByScore(String[] typ)
+ {
+ sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ }
+
+ private String[] getDisplayedFeatureTypes()
+ {
+ String[] typ = null;
+ if (fr != null)
+ {
+ synchronized (fr.renderOrder)
+ {
+ typ = new String[fr.renderOrder.length];
+ System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length);
+ for (int i = 0; i < typ.length; i++)
+ {
+ if (af.viewport.featuresDisplayed.get(typ[i]) == null)
+ {
+ typ[i] = null;
+ }
+ }
+ }
+ }
+ return typ;
+ }
+
+ private String[] getDisplayedFeatureGroups()
+ {
+ String[] gps = null;
+ if (fr != null)
+ {
+
+ if (fr.featureGroups != null)
+ {
+ Enumeration en = fr.featureGroups.keys();
+ gps = new String[fr.featureColours.size()];
+ int g = 0;
+ boolean valid = false;
+ while (en.hasMoreElements())
+ {
+ String gp = (String) en.nextElement();
+ Boolean on = (Boolean) fr.featureGroups.get(gp);
+ if (on != null && on.booleanValue())
+ {
+ valid = true;
+ gps[g++] = gp;
+ }
+ }
+ while (g < gps.length)
+ {
+ gps[g++] = null;
+ }
+ if (!valid)
+ {
+ return null;
+ }
+ }
+ }
+ return gps;
+ }
+
public void fetchDAS_actionPerformed(ActionEvent e)
{
fetchDAS.setEnabled(false);
}
/**
+ * blocking call to initialise the das source browser
+ */
+ public void initDasSources()
+ {
+ dassourceBrowser.initDasSources();
+ }
+
+ /**
+ * examine the current list of das sources and return any matching the given
+ * nicknames in sources
+ *
+ * @param sources
+ * Vector of Strings to resolve to DAS source nicknames.
+ * @return sources that are present in source list.
+ */
+ public Vector resolveSourceNicknames(Vector sources)
+ {
+ return dassourceBrowser.resolveSourceNicknames(sources);
+ }
+
+ /**
+ * get currently selected das sources. ensure you have called initDasSources
+ * before calling this.
+ *
+ * @return vector of selected das source nicknames
+ */
+ public Vector getSelectedSources()
+ {
+ return dassourceBrowser.getSelectedSources();
+ }
+
+ /**
* properly initialise DAS fetcher and then initiate a new thread to fetch
* features from the named sources (rather than any turned on by default)
*
*/
public void fetchDasFeatures(Vector sources)
{
- Thread thr = new Thread(new Runnable()
- {
- public void run()
- {
- // this actually initialises the das source list
- dassourceBrowser.paintComponent(null); // yuk
- }
- });
- thr.start();
- while (dassourceBrowser.loadingDasSources
- || dassourceBrowser.dasSources == null)
- {
- try
- {
- Thread.sleep(10);
- } catch (Exception e)
- {
- }
- ;
- }
- Vector resolved = new Vector();
- if (sources != null)
- {
- for (int i = 0; i < dassourceBrowser.dasSources.length; i++)
- {
- if (sources.contains(dassourceBrowser.dasSources[i].getNickname()))
- {
- if (!resolved.contains(dassourceBrowser.dasSources[i]))
- {
- resolved.addElement(dassourceBrowser.dasSources[i]);
- }
- }
- }
- }
+ initDasSources();
+ Vector resolved = resolveSourceNicknames(sources);
if (resolved.size() == 0)
{
resolved = dassourceBrowser.getSelectedSources();
Object color, boolean isSelected, boolean hasFocus, int row,
int column)
{
- Color newColor = (Color) color;
- setBackground(newColor);
+ Color newColor;
+ color = fr.featureColours.get((String) table.getModel().getValueAt(
+ row, 0));
+ if (color instanceof GraduatedColor)
+ {
+ newColor = ((GraduatedColor) color).getMaxColor();
+ Color minCol = ((GraduatedColor) color).getMinColor();;
+ setBackground(newColor);
+ setToolTipText("RGB value: Max (" + newColor.getRed() + ", "
+ + newColor.getGreen() + ", " + newColor.getBlue()
+ + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+ + ", " + minCol.getBlue() + ")");
+ }
+ else
+ {
+ newColor = (Color) color;
+ setBackground(newColor);
+ setToolTipText("RGB value: " + newColor.getRed() + ", "
+ + newColor.getGreen() + ", " + newColor.getBlue());
+ }
if (isSelected)
{
if (selectedBorder == null)
setBorder(unselectedBorder);
}
- setToolTipText("RGB value: " + newColor.getRed() + ", "
- + newColor.getGreen() + ", " + newColor.getBlue());
return this;
}
}
git://source.jalview.org / jalview.git / blobdiff