*/
package jalview.gui;
-import jalview.analysis.AlignmentSorter;
import jalview.bin.Cache;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
-import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
+import java.util.Set;
import java.util.Vector;
import javax.help.HelpSetException;
Object[][] originalData;
+ private float originalTransparency;
+
final JInternalFrame frame;
JScrollPane scrollPane = new JScrollPane();
{
this.af = af;
fr = af.getFeatureRenderer();
-
- transparency.setMaximum(100 - (int) (fr.transparency * 100));
+ // allow transparency to be recovered
+ transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100));
try
{
if (SwingUtilities.isRightMouseButton(evt))
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
- evt.getY());
+ table.getValueAt(selectedRow, 1), fr.getMinMax(),
+ evt.getX(), evt.getY());
}
else if (evt.getClickCount() == 2)
{
if (evt.isPopupTrigger())
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
+ table.getValueAt(selectedRow, 1), fr.getMinMax(),
+ evt.getX(),
evt.getY());
}
}
dassourceBrowser = new DasSourceBrowser(this);
dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
- if (af.getViewport().getFeaturesDisplayed() == null
- || fr.renderOrder == null)
+ if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
{
fr.findAllFeatures(true); // display everything!
}
public void actionPerformed(ActionEvent e)
{
- me.sortByScore(new String[]
+ me.af.avc.sortAlignmentByFeatureScore(new String[]
{ type });
}
public void actionPerformed(ActionEvent e)
{
- me.sortByDens(new String[]
+ me.af.avc.sortAlignmentByFeatureDensity(new String[]
{ type });
}
synchronized public void setTableData()
{
- if (fr.featureGroups == null)
- {
- fr.featureGroups = new Hashtable();
- }
Vector allFeatures = new Vector();
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
if (!allGroups.contains(group))
{
allGroups.addElement(group);
- if (group != null)
- {
- checkGroupState(group);
- }
+ checkGroupState(group);
}
}
}
/**
+ * Synchronise gui group list and check visibility of group
*
* @param group
- * @return true if group has been seen before and is already added to set.
+ * @return true if group is visible
*/
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
- }
+ boolean visible = fr.checkGroupVisibility(group, true);
if (groupPanel == null)
{
if (alreadyAdded)
{
- return true;
+ return visible;
}
-
- 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));
{
public void itemStateChanged(ItemEvent evt)
{
- fr.featureGroups.put(check.getText(),
- new Boolean(check.isSelected()));
+ fr.setGroupVisibility(check.getText(), check.isSelected());
af.alignPanel.getSeqPanel().seqCanvas.repaint();
if (af.alignPanel.overviewPanel != null)
{
}
});
groupPanel.add(check);
- return false;
+ return visible;
}
boolean resettingTable = false;
continue;
}
- if (group == null || fr.featureGroups.get(group) == null
- || ((Boolean) fr.featureGroups.get(group)).booleanValue())
+ if (group == null || checkGroupState(group))
{
- if (group != null)
- {
- checkGroupState(group);
- }
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
{
Object[][] data = new Object[fSize][3];
int dataIndex = 0;
- if (fr.renderOrder != null)
+ if (fr.hasRenderOrder())
{
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
}
- // 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--)
+ List<String> frl = fr.getRenderOrder();
+ for (int ro = frl.size() - 1; ro > -1; ro--)
{
- type = fr.renderOrder[ro];
+ type = frl.get(ro);
if (!visibleChecks.contains(type))
{
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getFeatureStyle(type);
- data[dataIndex][2] = new Boolean(
- af.getViewport().getFeaturesDisplayed().containsKey(type));
+ data[dataIndex][2] = new Boolean(af.getViewport()
+ .getFeaturesDisplayed().isVisible(type));
dataIndex++;
visibleChecks.removeElement(type);
}
if (data[dataIndex][1] == null)
{
// "Colour has been updated in another view!!"
- fr.renderOrder = null;
+ fr.clearRenderOrder();
return;
}
if (groupPanel != null)
{
- groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
- 4));
+ groupPanel.setLayout(new GridLayout(
+ fr.getFeatureGroupsSize() / 4 + 1, 4));
groupPanel.validate();
bigPanel.add(groupPanel, BorderLayout.NORTH);
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
- Iterator e = fr.featureColours.keySet().iterator();
- float[] sortOrder = new float[fr.featureColours.size()];
- String[] sortTypes = new String[fr.featureColours.size()];
+ Set fr_colours = fr.getAllFeatureColours();
+ Iterator e = fr_colours.iterator();
+ float[] sortOrder = new float[fr_colours.size()];
+ String[] sortTypes = new String[fr_colours.size()];
int i = 0;
while (e.hasNext())
{
{
public void actionPerformed(ActionEvent e)
{
- sortByScore(null);
+ af.avc.sortAlignmentByFeatureScore(null);
}
});
sortByDens.setFont(JvSwingUtils.getLabelFont());
{
public void actionPerformed(ActionEvent e)
{
- sortByDens(null);
+ af.avc.sortAlignmentByFeatureDensity(null);
+ }
+ });
+ help.setFont(JvSwingUtils.getLabelFont());
+ help.setText(MessageManager.getString("action.help"));
+ help.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.SequenceFeatureSettings);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
}
});
help.setFont(JvSwingUtils.getLabelFont());
{
public void actionPerformed(ActionEvent e)
{
+ fr.setTransparency(originalTransparency);
updateFeatureRenderer(originalData);
close();
}
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)
- {
- ArrayList types = new ArrayList();
- for (int i = 0; i < typ.length; i++)
- {
- if (typ[i] != null)
- {
- types.add(typ[i]);
- }
- typ = new String[types.size()];
- types.toArray(typ);
- }
- }
- if (gps != null)
- {
- ArrayList grps = new ArrayList();
-
- for (int i = 0; i < gps.length; i++)
- {
- if (gps[i] != null)
- {
- grps.add(gps[i]);
- }
- }
- gps = new String[grps.size()];
- grps.toArray(gps);
- }
- 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.getFeaturesDisplayed().get(typ[i]) == null)
- {
- typ[i] = null;
- }
- }
- }
- }
- return typ;
- }
-
- private String[] getDisplayedFeatureGroups()
- {
- String[] gps = null;
- ArrayList<String> _gps = new ArrayList<String>();
- if (fr != null)
- {
-
- if (fr.featureGroups != null)
- {
- Iterator en = fr.featureGroups.keySet().iterator();
- int g = 0;
- boolean valid = false;
- while (en.hasNext())
- {
- String gp = (String) en.next();
- Boolean on = (Boolean) fr.featureGroups.get(gp);
- if (on != null && on.booleanValue())
- {
- valid = true;
- _gps.add(gp);
- }
- }
- if (!valid)
- {
- return null;
- }
- else
- {
- gps = new String[_gps.size()];
- _gps.toArray(gps);
- }
- }
- }
- return gps;
- }
-
public void fetchDAS_actionPerformed(ActionEvent e)
{
fetchDAS.setEnabled(false);
git://source.jalview.org / jalview.git / blobdiff