import java.awt.*;
import java.awt.event.*;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
import javax.swing.*;
import javax.swing.event.*;
import javax.swing.table.*;
extends JPanel
{
DasSourceBrowser dassourceBrowser;
- jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
+ jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
JPanel settingsPane = new JPanel();
JPanel dasSettingsPane = new JPanel();
if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
{
- fr.findAllFeatures();
+ fr.findAllFeatures(true); // display everything!
}
setTableData();
+ final PropertyChangeListener change;
+ final FeatureSettings fs=this;
+ fr.addPropertyChangeListener(change=new PropertyChangeListener() {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (!fs.resettingTable && !fs.handlingUpdate) {
+ fs.handlingUpdate=true;
+ fs.resetTable(null); // new groups may be added with new seuqence feature types only
+ fs.handlingUpdate=false;
+ }
+ }
+
+ });
frame = new JInternalFrame();
frame.setContentPane(this);
Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ }
+ ;
+ });
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
+ /**
+ * true when Feature Settings are updating from feature renderer
+ */
+ private boolean handlingUpdate=false;
+ /**
+ * contains a float[3] for each feature type string. created by setTableData
+ */
+ Hashtable typeWidth=null;
synchronized public void setTableData()
{
if (fr.featureGroups == null)
{
fr.featureGroups = new Hashtable();
}
-
Vector allFeatures = new Vector();
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
String group;
-
for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
{
if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().
if (!allGroups.contains(group))
{
allGroups.addElement(group);
-
- boolean visible = true;
- if (fr.featureGroups.containsKey(group))
- {
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
- }
-
- if (groupPanel == null)
- {
- groupPanel = new JPanel();
- }
-
- boolean alreadyAdded = false;
- for (int g = 0; g < groupPanel.getComponentCount(); g++)
- {
- if ( ( (JCheckBox) groupPanel.getComponent(g))
- .getText().equals(group))
- {
- alreadyAdded = true;
- break;
- }
- }
-
- if (alreadyAdded)
+ if (group!=null)
{
- continue;
+ checkGroupState(group);
}
-
- fr.featureGroups.put(group, new Boolean(visible));
-
- final JCheckBox check = new JCheckBox(group, visible);
- check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- fr.featureGroups.put(check.getText(),
- new Boolean(check.isSelected()));
- af.alignPanel.seqPanel.seqCanvas.repaint();
- if (af.alignPanel.overviewPanel != null)
- {
- af.alignPanel.overviewPanel.updateOverviewImage();
- }
-
- resetTable(true);
- }
- });
- groupPanel.add(check);
}
}
}
}
- resetTable(false);
+ resetTable(null);
validate();
}
+ /**
+ *
+ * @param group
+ * @return true if group has been seen before and is already added to set.
+ */
+ private boolean checkGroupState(String group) {
+ boolean visible;
+ if (fr.featureGroups.containsKey(group))
+ {
+ visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+ } else {
+ visible=true; // new group is always made visible
+ }
+
+ if (groupPanel == null)
+ {
+ groupPanel = new JPanel();
+ }
+
+ boolean alreadyAdded = false;
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ if ( ( (JCheckBox) groupPanel.getComponent(g))
+ .getText().equals(group))
+ {
+ alreadyAdded = true;
+ ((JCheckBox)groupPanel.getComponent(g)).setSelected(visible);
+ break;
+ }
+ }
- void resetTable(boolean groupsChanged)
+ if (alreadyAdded)
+ {
+
+ return true;
+ }
+
+ fr.featureGroups.put(group, new Boolean(visible));
+ final String grp = group;
+ final JCheckBox check = new JCheckBox(group, visible);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
+ fr.featureGroups.put(check.getText(),
+ new Boolean(check.isSelected()));
+ af.alignPanel.seqPanel.seqCanvas.repaint();
+ if (af.alignPanel.overviewPanel != null)
+ {
+ af.alignPanel.overviewPanel.updateOverviewImage();
+ }
+
+ resetTable(new String[] { grp } );
+ }
+ });
+ groupPanel.add(check);
+ return false;
+ }
+ boolean resettingTable=false;
+ synchronized void resetTable(String[] groupChanged)
{
+ if (resettingTable==true)
+ {
+ return;
+ }
+ resettingTable=true;
+ typeWidth=new Hashtable();
+ // 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();
//Find out which features should be visible depending on which groups
//are selected / deselected
+ //and recompute average width ordering
for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
{
if (group == null || fr.featureGroups.get(group) == null ||
( (Boolean) fr.featureGroups.get(group)).booleanValue())
{
+ if (group!=null)
+ checkGroupState(group);
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
{
visibleChecks.addElement(type);
}
}
+ if (!typeWidth.containsKey(tmpfeatures[index].getType())) {
+ typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]);
+ } else {
+ avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
+ }
+ avWidth[0]++;
+ if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
+ {
+ avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
+ } else {
+ avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
+ }
index++;
}
}
if (fr.renderOrder != null)
{
+ if (!handlingUpdate)
+ fr.findAllFeatures(groupChanged!=null); // prod to update 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--)
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getColour(type);
- data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.
- containsKey(type));
+ data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
dataIndex++;
visibleChecks.removeElement(type);
}
bigPanel.add(groupPanel, BorderLayout.NORTH);
}
- updateFeatureRenderer(data);
-
+ updateFeatureRenderer(data, groupChanged!=null);
+ resettingTable=false;
+ }
+ /**
+ * reorder data based on the featureRenderers global priority list.
+ * @param data
+ */
+ private void ensureOrder(Object[][] data)
+ {
+ boolean sort=false;
+ float[] order = new float[data.length];
+ for (int i=0;i<order.length; i++)
+ {
+ order[i] = fr.getOrder(data[i][0].toString());
+ if (order[i]<0)
+ order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
+ if (i>1)
+ sort = sort || order[i-1]>order[i];
+ }
+ if (sort)
+ jalview.util.QuickSort.sort(order, data);
}
void load()
JalviewUserColours();
jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
- for (int i = 0; i < jucs.getColourCount(); i++)
+ for (int i = jucs.getColourCount()-1; i >=0; i--)
{
- fr.setColour(jucs.getColour(i).getName(),
+ String name;
+ fr.setColour(name=jucs.getColour(i).getName(),
new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
16)));
+ fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
+ }
+ if (table!=null) {
+ resetTable(null);
+ Object[][] data=((FeatureTableModel) table.getModel()).getData();
+ ensureOrder(data);
+ updateFeatureRenderer(data,false);
+ table.repaint();
}
-
- setTableData();
- af.alignPanel.paintAlignment(true);
}
catch (Exception ex)
{
new FileOutputStream(choice), "UTF-8"));
Enumeration e = fr.featureColours.keys();
+ float[] sortOrder = new float[fr.featureColours.size()];
+ String[] sortTypes = new String[fr.featureColours.size()];
+ int i=0;
while (e.hasMoreElements())
{
+ sortTypes[i] = e.nextElement().toString();
+ sortOrder[i] = fr.getOrder(sortTypes[i]);
+ i++;
+ }
+ jalview.util.QuickSort.sort(sortOrder, sortTypes);
+ sortOrder=null;
+ for (i=0; i<sortTypes.length; i++) {
jalview.binding.Colour col = new jalview.binding.Colour();
- col.setName(e.nextElement().toString());
+ col.setName(sortTypes[i]);
col.setRGB(jalview.util.Format.getHexString(
fr.getColour(col.getName())));
ucs.addColour(col);
}
-
ucs.marshal(out);
out.close();
}
i, 2);
}
}
+ public void orderByAvWidth() {
+ if (table==null || table.getModel()==null)
+ return;
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ float[] width = new float[data.length];
+ float[] awidth;
+ float max=0;
+ int num=0;
+ for (int i=0;i<data.length;i++) {
+ awidth = (float[]) typeWidth.get(data[i][0]);
+ 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])
+ //if (width[i]==1) // hack to distinguish single width sequences.
+ num++;
+ } else {
+ width[i]=0;
+ }
+ if (max<width[i])
+ max=width[i];
+ }
+ boolean sort=false;
+ for (int i=0;i<width.length; i++) {
+ //awidth = (float[]) typeWidth.get(data[i][0]);
+ if (width[i]==0)
+ {
+ width[i] = fr.getOrder(data[i][0].toString());
+ if (width[i]<0)
+ {
+ width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
+ }
+ } else {
+ width[i] /=max; // normalize
+ fr.setOrder(data[i][0].toString(), width[i]); // store for later
+ }
+ if (i>0)
+ sort = sort || width[i-1]>width[i];
+ }
+ if (sort)
+ jalview.util.QuickSort.sort(width, data);
+ // update global priority order
+ updateFeatureRenderer(data,false);
+ table.repaint();
+ }
public void close()
{
try
public void updateFeatureRenderer(Object[][] data)
{
- fr.setFeaturePriority(data);
+ updateFeatureRenderer(data, true);
+ }
+ private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+ {
+ fr.setFeaturePriority(data, visibleNew);
af.alignPanel.paintAlignment(true);
-
- if (af.alignPanel.overviewPanel != null)
- {
- af.alignPanel.overviewPanel.updateOverviewImage();
- }
}
int selectedRow = -1;
JButton fetchDAS = new JButton();
JButton saveDAS = new JButton();
JButton cancelDAS = new JButton();
+ JButton optimizeOrder = new JButton();
+ JPanel transbuttons = new JPanel(new BorderLayout());
private void jbInit()
throws Exception
{
invertSelection();
}
});
+ optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ optimizeOrder.setText("Optimise Order");
+ optimizeOrder.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ orderByAvWidth();
+ }
+ });
cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
cancel.setText("Cancel");
cancel.addActionListener(new ActionListener()
tabbedPane.addTab("DAS Settings", dasSettingsPane);
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
transPanel.add(transparency);
- transPanel.add(invert);
+ transbuttons.add(invert, java.awt.BorderLayout.NORTH);
+ transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH);
+ transPanel.add(transbuttons);
buttonPanel.add(ok);
buttonPanel.add(cancel);
buttonPanel.add(loadColours);
}
dasFeatureFetcher =
- new jalview.io.DasSequenceFeatureFetcher(
+ new jalview.ws.DasSequenceFeatureFetcher(
dataset,
this,
selectedSources);
fetchDAS.setEnabled(true);
cancelDAS.setEnabled(false);
}
+ public void noDasSourceActive()
+ {
+ JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "No das sources were selected.\n"
+ + "Please select some sources and\n"
+ +" try again.",
+ "No Sources Selected",
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.INFORMATION_MESSAGE);
+ complete();
+ }
/////////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
return this;
}
}
+
}
class ColorEditor
git://source.jalview.org / jalview.git / blobdiff