package jalview.appletgui;
import java.util.*;
-
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
ScrollPane scrollPane;
- boolean alignmentHasFeatures = false;
-
Image linkImage;
Scrollbar transparency;
fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
transparency = new Scrollbar(Scrollbar.HORIZONTAL,
- 100 - (int) (fr.transparency * 100), 1, 1, 100);
+ 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
- if (fr.transparencySetter != null)
+ if (fr.isTransparencyAvailable())
{
transparency.addAdjustmentListener(this);
}
linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
}
- if (av.featuresDisplayed == null)
+ if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())
{
- fr.findAllFeatures();
+ fr.findAllFeatures(true); // was default - now true to make all visible
}
setTableData();
this.setLayout(new BorderLayout());
scrollPane = new ScrollPane();
scrollPane.add(featurePanel);
- if (alignmentHasFeatures)
+ if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
{
add(scrollPane, BorderLayout.CENTER);
}
Panel tPanel = new Panel(new BorderLayout());
- if (fr.transparencySetter != null)
+ if (fr.isTransparencyAvailable())
{
tPanel.add(transparency, BorderLayout.CENTER);
tPanel.add(new Label("Transparency"), BorderLayout.EAST);
{
groupPanel
.setLayout(new GridLayout(
- (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1,
- 4));
+ (fr.getFeatureGroupsSize()) / 4 + 1,
+ 4)); // JBPNote - this was scaled on number of visible groups. seems broken
groupPanel.validate();
add(groupPanel, BorderLayout.NORTH);
public void actionPerformed(ActionEvent e)
{
- me.sortByScore(new String[]
+ me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
{ type });
}
public void actionPerformed(ActionEvent e)
{
- me.sortByDens(new String[]
+ me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
{ type });
}
public void setTableData()
{
- alignmentHasFeatures = fr.buildGroupHash();
- if (alignmentHasFeatures)
+ if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
{
rebuildGroups();
}
// TODO: JAL-964 - smoothly incorporate new group entries if panel already
// displayed and new groups present
- Enumeration gps = fr.featureGroups.keys();
- while (gps.hasMoreElements())
+ for (String group:(List<String>)fr.getFeatureGroups())
{
- String group = (String) gps.nextElement();
- Boolean vis = (Boolean) fr.featureGroups.get(group);
- Checkbox check = new MyCheckbox(group, vis.booleanValue(),
+ boolean vis = fr.checkGroupVisibility(group, false);
+ Checkbox check = new MyCheckbox(group, vis,
(fr.featureLinks != null && fr.featureLinks
.containsKey(group)));
check.addMouseListener(this);
check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(this);
- check.setVisible(fr.hiddenGroups.contains(group));
+ check.addItemListener(groupItemListener);
+ // note - visibility seems to correlate with displayed. ???wtf ??
+ check.setVisible(vis);
groupPanel.add(check);
}
if (rdrw)
groupPanel.validate();
}
}
-
// This routine adds and removes checkboxes depending on
// Group selection states
void resetTable(boolean groupsChanged)
{
group = tmpfeatures[index].featureGroup;
- if (group == null || fr.featureGroups.get(group) == null
- || ((Boolean) fr.featureGroups.get(group)).booleanValue())
+ if (group == null || fr.checkGroupVisibility(group, true))
{
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
}
}
- if (fr.renderOrder != null)
+ if (fr.getRenderOrder() != null)
{
// 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> rol = fr.getRenderOrder();
+ for (int ro = rol.size() - 1; ro > -1; ro--)
{
- String item = fr.renderOrder[ro];
+ String item = rol.get(ro);
if (!visibleChecks.contains(item))
{
if (addCheck)
{
boolean selected = false;
- if (groupsChanged || av.featuresDisplayed.containsKey(type))
+ if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
{
selected = true;
}
selectionChanged();
}
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt != null)
- {
- // Is the source a top level featureGroup?
+ private ItemListener groupItemListener = new ItemListener() {
+ public void itemStateChanged(ItemEvent evt) {
Checkbox source = (Checkbox) evt.getSource();
- if (fr.featureGroups.containsKey(source.getLabel()))
+ fr.setGroupVisibility(source.getLabel(),
+ source.getState());
+ ap.seqPanel.seqCanvas.repaint();
+ if (ap.overviewPanel != null)
{
- fr.featureGroups.put(source.getLabel(),
- new Boolean(source.getState()));
- ap.seqPanel.seqCanvas.repaint();
- if (ap.overviewPanel != null)
- {
- ap.overviewPanel.updateOverviewImage();
- }
-
- resetTable(true);
- return;
+ ap.overviewPanel.updateOverviewImage();
}
- }
+ resetTable(true);
+ return;
+ };
+ };
+ public void itemStateChanged(ItemEvent evt)
+ {
selectionChanged();
}
MyCheckbox check = (MyCheckbox) evt.getSource();
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
{
- this.popupSort(check, fr.minmax, evt.getX(), evt.getY());
+ this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
}
if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
{
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- fr.transparency = ((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
ap.seqPanel.seqCanvas.repaint();
}
}
}
- protected void sortByDens(String[] typ)
- {
- sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
- }
-
- 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 (av.featuresDisplayed.get(typ[i]) == null)
- {
- typ[i] = null;
- }
- }
- }
- }
- return typ;
- }
-
- protected void sortBy(String[] typ, String methodText, final String method)
- {
- if (typ == null)
- {
- typ = getDisplayedFeatureTypes();
- }
- String gps[] = null;
- gps = fr.getGroups(true);
- 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 = ap;
- 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);
- this.ap.alignFrame.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);
- }
-
}
git://source.jalview.org / jalview.git / blobdiff