extends JPanel
{
DasSourceBrowser dassourceBrowser;
- jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
+ jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
JPanel settingsPane = new JPanel();
JPanel dasSettingsPane = new JPanel();
{
if (!fs.resettingTable && !fs.handlingUpdate) {
fs.handlingUpdate=true;
- fs.resetTable(new String[] {}); // groups may be added
+ 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);
* 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
*/
if (!allGroups.contains(group))
{
allGroups.addElement(group);
-
- boolean visible;
- if (fr.featureGroups.containsKey(group))
+ if (group!=null)
{
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
- } else {
- visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType());
+ checkGroupState(group);
}
-
- 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)
- {
-
- continue;
- }
-
- 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 (!visibleChecks.contains(type))
{
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;
fetchDAS.setEnabled(false);
cancelDAS.setEnabled(true);
Vector selectedSources = dassourceBrowser.getSelectedSources();
-
+ doDasFeatureFetch(selectedSources, true, true);
+ }
+ /**
+ * get the features from selectedSources for all or the current selection
+ * @param selectedSources
+ * @param checkDbRefs
+ * @param promptFetchDbRefs
+ */
+ private void doDasFeatureFetch(Vector selectedSources, boolean checkDbRefs, boolean promptFetchDbRefs)
+ {
SequenceI[] dataset, seqs;
int iSize;
-
- if (af.getViewport().getSelectionGroup() != null
- && af.getViewport().getSelectionGroup().getSize() > 0)
+ AlignViewport vp = af.getViewport();
+ if (vp.getSelectionGroup() != null
+ && vp.getSelectionGroup().getSize() > 0)
{
- iSize = af.getViewport().getSelectionGroup().getSize();
+ iSize = vp.getSelectionGroup().getSize();
dataset = new SequenceI[iSize];
- seqs = af.getViewport().getSelectionGroup().
+ seqs = vp.getSelectionGroup().
getSequencesInOrder(
- af.getViewport().getAlignment());
+ vp.getAlignment());
}
else
{
- iSize = af.getViewport().getAlignment().getHeight();
- seqs = af.getViewport().getAlignment().getSequencesArray();
+ iSize = vp.getAlignment().getHeight();
+ seqs = vp.getAlignment().getSequencesArray();
}
dataset = new SequenceI[iSize];
dataset[i] = seqs[i].getDatasetSequence();
}
+ cancelDAS.setEnabled(true);
dasFeatureFetcher =
- new jalview.io.DasSequenceFeatureFetcher(
+ new jalview.ws.DasSequenceFeatureFetcher(
dataset,
this,
- selectedSources);
- cancelDAS.setEnabled(true);
+ selectedSources, checkDbRefs, promptFetchDbRefs);
af.getViewport().setShowSequenceFeatures(true);
af.showSeqFeatures.setSelected(true);
}
+ /**
+ * properly initialise DAS fetcher and then initiate a new thread to fetch features from the named sources (rather than any turned on by default)
+ * @param sources
+ */
+ 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]);
+ }
+ }
+ }
+ }
+ if (resolved.size()==0)
+ {
+ resolved = dassourceBrowser.getSelectedSources();
+ }
+ if (resolved.size()>0)
+ {
+ final Vector dassources = resolved;
+ SwingUtilities.invokeLater(new Runnable() {
+
+ public void run()
+ {
+ fetchDAS.setEnabled(false);
+ cancelDAS.setEnabled(true);
+ doDasFeatureFetch(dassources, true, false);
+
+ }});
+ }
+ }
public void saveDAS_actionPerformed(ActionEvent e)
{
public void cancelDAS_actionPerformed(ActionEvent e)
{
- dasFeatureFetcher.cancel();
+ if (dasFeatureFetcher!=null)
+ {
+ dasFeatureFetcher.cancel();
+ }
fetchDAS.setEnabled(true);
cancelDAS.setEnabled(false);
}
+ public void noDasSourceActive()
+ {
+ complete();
+ 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);
+ }
/////////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
git://source.jalview.org / jalview.git / blobdiff