extends JPanel
{
DasSourceBrowser dassourceBrowser;
- jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
+ jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
JPanel settingsPane = new JPanel();
JPanel dasSettingsPane = new JPanel();
final PropertyChangeListener change;
final FeatureSettings fs=this;
fr.addPropertyChangeListener(change=new PropertyChangeListener() {
- private boolean firing=false;
public void propertyChange(PropertyChangeEvent evt)
{
- if (!fs.resettingTable && !firing) {
- firing=true;
- resetTable(null);
- firing=false;
+ 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.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;
if (!allGroups.contains(group))
{
allGroups.addElement(group);
-
- boolean visible;
- if (fr.featureGroups.containsKey(group))
- {
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
- } else {
- visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType());
- }
-
- 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 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);
}
}
index++;
}
}
-
+
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;
+ }
+ }
+
+ 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;
- void resetTable(String[] groupChanged)
+ synchronized void resetTable(String[] groupChanged)
{
+ if (resettingTable==true)
+ {
+ return;
+ }
resettingTable=true;
typeWidth=new Hashtable();
- Vector groupchanged = new Vector();
// TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
float[] avWidth=null;
SequenceFeature[] tmpfeatures;
if (group == null || fr.featureGroups.get(group) == null ||
( (Boolean) fr.featureGroups.get(group)).booleanValue())
{
+ if (group!=null)
+ checkGroupState(group);
type = tmpfeatures[index].getType();
- if (groupchanged==null || groupchanged.contains(group)) {
- //af.getViewport().featuresDisplayed.put(type, fr.getColour(type));
- }
if (!visibleChecks.contains(type))
{
visibleChecks.addElement(type);
if (fr.renderOrder != null)
{
- fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
+ 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--)
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--)
{
String name;
fr.setColour(name=jucs.getColour(i).getName(),
new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
16)));
- fr.setOrder(name,i/jucs.getColourCount());
+ 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();
}
boolean sort=false;
for (int i=0;i<width.length; i++) {
//awidth = (float[]) typeWidth.get(data[i][0]);
- if (width[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 {
+ } else {
width[i] /=max; // normalize
- fr.setOrder(data[i][0].toString(), width[i]); // store for later
+ 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();
}
{
fr.setFeaturePriority(data, visibleNew);
af.alignPanel.paintAlignment(true);
-
- if (af.alignPanel.overviewPanel != null)
- {
- af.alignPanel.overviewPanel.updateOverviewImage();
- }
}
int selectedRow = -1;
}
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