/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.TYPE_COLUMN;
+
+import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.MouseMotionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
-import java.util.Vector;
+import java.util.Map;
+import java.util.Set;
-public class FeatureSettings extends Panel implements ItemListener,
- MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener, FeatureSettingsControllerI
+public class FeatureSettings extends Panel
+ implements ItemListener, MouseListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
transparency = new Scrollbar(Scrollbar.HORIZONTAL,
100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
- if (fr.isTransparencyAvailable())
- {
- transparency.addAdjustmentListener(this);
- }
- else
- {
- transparency.setEnabled(false);
- }
+ transparency.addAdjustmentListener(this);
java.net.URL url = getClass().getResource("/images/link.gif");
if (url != null)
{
fr.findAllFeatures(true); // was default - now true to make all visible
}
+ groupPanel = new Panel();
discoverAllFeatureData();
Panel tPanel = new Panel(new BorderLayout());
- if (fr.isTransparencyAvailable())
- {
- tPanel.add(transparency, BorderLayout.CENTER);
- tPanel.add(new Label("Transparency"), BorderLayout.EAST);
- }
- else
- {
- tPanel.add(
- new Label("Transparency not available in this web browser"),
- BorderLayout.CENTER);
- }
+ tPanel.add(transparency, BorderLayout.CENTER);
+ tPanel.add(new Label("Transparency"), BorderLayout.EAST);
lowerPanel.add(tPanel, BorderLayout.SOUTH);
add(lowerPanel, BorderLayout.SOUTH);
- if (groupPanel != null)
- {
- groupPanel.setLayout(new GridLayout(
- (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
- // scaled on number of
- // visible groups. seems
- // broken
- groupPanel.validate();
+ groupPanel.setLayout(
+ new GridLayout((fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote
+ // - this
+ // was
+ // scaled
+ // on
+ // number
+ // of
+ // visible
+ // groups.
+ // seems
+ // broken
+ groupPanel.validate();
+
+ add(groupPanel, BorderLayout.NORTH);
- add(groupPanel, BorderLayout.NORTH);
- }
frame = new Frame();
frame.add(this);
final FeatureSettings me = this;
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
if (me.av.featureSettings == me)
width, height);
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.black);
- g.drawString(MessageManager
- .getString("label.no_features_added_to_this_alignment"), 10, 20);
- g.drawString(MessageManager
- .getString("label.features_can_be_added_from_searches_1"), 10,
- 40);
- g.drawString(MessageManager
- .getString("label.features_can_be_added_from_searches_2"), 10,
- 60);
+ g.drawString(MessageManager.getString(
+ "label.no_features_added_to_this_alignment"), 10, 20);
+ g.drawString(MessageManager.getString(
+ "label.features_can_be_added_from_searches_1"), 10, 40);
+ g.drawString(MessageManager.getString(
+ "label.features_can_be_added_from_searches_2"), 10, 60);
}
- protected void popupSort(final MyCheckbox check, final Hashtable minmax,
- int x, int y)
+ protected void popupSort(final MyCheckbox check,
+ final Map<String, float[][]> minmax, int x, int y)
{
final String type = check.type;
- final Object typeCol = fr.getFeatureStyle(type);
- java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
- "label.settings_for_type", new String[] { type }));
+ final FeatureColourI typeCol = fr.getFeatureStyle(type);
+ PopupMenu men = new PopupMenu(MessageManager
+ .formatMessage("label.settings_for_type", new String[]
+ { type }));
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
scr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
me.ap.alignFrame.avc
- .sortAlignmentByFeatureScore(new String[] { type });
+ .sortAlignmentByFeatureScore(Arrays.asList(new String[]
+ { type }));
}
});
dens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
me.ap.alignFrame.avc
- .sortAlignmentByFeatureDensity(new String[] { type });
+ .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ { type }));
}
});
men.add(dens);
+
if (minmax != null)
{
- final Object typeMinMax = minmax.get(type);
+ final float[][] typeMinMax = minmax.get(type);
/*
* final java.awt.CheckboxMenuItem chb = new
* java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
*
* }); men.add(chb);
*/
- if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+ if (typeMinMax != null && typeMinMax[0] != null)
{
// graduated colourschemes for those where minmax exists for the
// positional features
MenuItem mxcol = new MenuItem(
- (typeCol instanceof Color) ? "Graduated Colour"
+ (typeCol.isSimpleColour()) ? "Graduated Colour"
: "Single Colour");
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- if (typeCol instanceof Color)
+ if (typeCol.isSimpleColour())
{
new FeatureColourChooser(me, type);
// write back the current colour object to update the table
}
else
{
- new UserDefinedColours(me, check.type,
- ((GraduatedColor) typeCol));
+ new UserDefinedColours(me, check.type, typeCol);
}
}
});
}
}
+
+ MenuItem selectContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_containing"));
+ selectContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+ false, type);
+ }
+ });
+ men.add(selectContaining);
+
+ MenuItem selectNotContaining = new MenuItem(MessageManager
+ .getString("label.select_columns_not_containing"));
+ selectNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+ false, type);
+ }
+ });
+ men.add(selectNotContaining);
+
+ MenuItem hideContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_containing"));
+ hideContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, true);
+ }
+ });
+ men.add(hideContaining);
+
+ MenuItem hideNotContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_not_containing"));
+ hideNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, false);
+ }
+ });
+ men.add(hideNotContaining);
+
this.featurePanel.add(men);
men.show(this.featurePanel, x, y);
}
if (fr.getAllFeatureColours() != null
&& fr.getAllFeatureColours().size() > 0)
{
- rebuildGroups();
+ // rebuildGroups();
}
resetTable(false);
}
/**
- * rebuilds the group panel
+ * Answers the visibility of the given group, and adds a checkbox for it if
+ * there is not one already
*/
- public void rebuildGroups()
+ public boolean checkGroupState(String group)
{
- boolean rdrw = false;
- if (groupPanel == null)
- {
- groupPanel = new Panel();
- }
- else
- {
- rdrw = true;
- groupPanel.removeAll();
- }
- // TODO: JAL-964 - smoothly incorporate new group entries if panel already
- // displayed and new groups present
- for (String group : fr.getFeatureGroups())
- {
- 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(groupItemListener);
- // note - visibility seems to correlate with displayed. ???wtf ??
- check.setVisible(vis);
- groupPanel.add(check);
- }
- if (rdrw)
+ boolean visible = fr.checkGroupVisibility(group, true);
+
+ /*
+ * is there already a checkbox for this group?
+ */
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
{
- groupPanel.validate();
+ if (((Checkbox) groupPanel.getComponent(g)).getLabel().equals(group))
+ {
+ ((Checkbox) groupPanel.getComponent(g)).setState(visible);
+ return visible;
+ }
}
+
+ /*
+ * add a new checkbox
+ */
+ Checkbox check = new MyCheckbox(group, visible, false);
+ check.addMouseListener(this);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(groupItemListener);
+ groupPanel.add(check);
+
+ groupPanel.validate();
+ return visible;
}
// This routine adds and removes checkboxes depending on
// Group selection states
void resetTable(boolean groupsChanged)
{
- SequenceFeature[] tmpfeatures;
- String group = null, type;
- Vector visibleChecks = new Vector();
+ List<String> displayableTypes = new ArrayList<>();
+ Set<String> foundGroups = new HashSet<>();
+
AlignmentI alignment = av.getAlignment();
+
for (int i = 0; i < alignment.getHeight(); i++)
{
- if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
+ SequenceI seq = alignment.getSequenceAt(i);
- tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
+ /*
+ * get the sequence's groups for positional features
+ * and keep track of which groups are visible
+ */
+ Set<String> groups = seq.getFeatures().getFeatureGroups(true);
+ Set<String> visibleGroups = new HashSet<>();
+ for (String group : groups)
{
- group = tmpfeatures[index].featureGroup;
-
- if (group == null || fr.checkGroupVisibility(group, true))
+ // if (group == null || fr.checkGroupVisibility(group, true))
+ if (group == null || checkGroupState(group))
{
- type = tmpfeatures[index].getType();
- if (!visibleChecks.contains(type))
- {
- visibleChecks.addElement(type);
- }
+ visibleGroups.add(group);
}
- index++;
}
+ foundGroups.addAll(groups);
+
+ /*
+ * get distinct feature types for visible groups
+ * record distinct visible types
+ */
+ Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
+ visibleGroups.toArray(new String[visibleGroups.size()]));
+ displayableTypes.addAll(types);
}
+ /*
+ * remove any checkboxes for groups not present
+ */
+ pruneGroups(foundGroups);
+
Component[] comps;
int cSize = featurePanel.getComponentCount();
MyCheckbox check;
{
comps = featurePanel.getComponents();
check = (MyCheckbox) comps[i];
- if (!visibleChecks.contains(check.type))
+ if (!displayableTypes.contains(check.type))
{
featurePanel.remove(i);
cSize--;
{
String item = rol.get(ro);
- if (!visibleChecks.contains(item))
+ if (!displayableTypes.contains(item))
{
continue;
}
- visibleChecks.removeElement(item);
+ displayableTypes.remove(item);
addCheck(false, item);
}
}
- // now add checkboxes which should be visible,
- // if they have not already been added
- Enumeration en = visibleChecks.elements();
-
- while (en.hasMoreElements())
+ /*
+ * now add checkboxes which should be visible,
+ * if they have not already been added
+ */
+ for (String type : displayableTypes)
{
- addCheck(groupsChanged, en.nextElement().toString());
+ addCheck(groupsChanged, type);
}
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
- 1, 10, 5));
+ featurePanel.setLayout(
+ new GridLayout(featurePanel.getComponentCount(), 1, 10, 5));
featurePanel.validate();
if (scrollPane != null)
}
/**
+ * Remove from the groups panel any checkboxes for groups that are not in the
+ * foundGroups set. This enables removing a group from the display when the
+ * last feature in that group is deleted.
+ *
+ * @param foundGroups
+ */
+ protected void pruneGroups(Set<String> foundGroups)
+ {
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ Checkbox checkbox = (Checkbox) groupPanel.getComponent(g);
+ if (!foundGroups.contains(checkbox.getLabel()))
+ {
+ groupPanel.remove(checkbox);
+ }
+ }
+ }
+
+ /**
* update the checklist of feature types with the given type
*
* @param groupsChanged
selected = true;
}
- check = new MyCheckbox(
- type,
- selected,
- (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+ check = new MyCheckbox(type, selected, false,
fr.getFeatureStyle(type));
check.addMouseListener(this);
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
for (int i = 0; i < featurePanel.getComponentCount(); i++)
Checkbox check = (Checkbox) featurePanel.getComponent(i);
check.setState(!check.getState());
}
- selectionChanged();
+ selectionChanged(true);
}
private ItemListener groupItemListener = new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
Checkbox source = (Checkbox) evt.getSource();
};
};
+ @Override
public void itemStateChanged(ItemEvent evt)
{
- selectionChanged();
+ selectionChanged(true);
}
- void selectionChanged()
+ void selectionChanged(boolean updateOverview)
{
Component[] comps = featurePanel.getComponents();
int cSize = comps.length;
- Object[][] tmp = new Object[cSize][3];
+ /*
+ * temporary! leave column[2] empty - used for Filter in
+ * gui.FeatureSettings
+ */
+ int columnCount = 4;
+ Object[][] tmp = new Object[cSize][columnCount];
int tmpSize = 0;
for (int i = 0; i < cSize; i++)
{
MyCheckbox check = (MyCheckbox) comps[i];
- tmp[tmpSize][0] = check.type;
- tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
- tmp[tmpSize][2] = new Boolean(check.getState());
+ tmp[tmpSize][TYPE_COLUMN /* 0 */] = check.type;
+ tmp[tmpSize][COLOUR_COLUMN /* 1 */] = fr.getFeatureStyle(check.type);
+ tmp[tmpSize][SHOW_COLUMN /* 3 */] = new Boolean(check.getState());
tmpSize++;
}
- Object[][] data = new Object[tmpSize][3];
+ Object[][] data = new Object[tmpSize][columnCount];
System.arraycopy(tmp, 0, data, 0, tmpSize);
fr.setFeaturePriority(data);
- ap.paintAlignment(true);
+ ap.paintAlignment(updateOverview, updateOverview);
}
MyCheckbox selectedCheck;
boolean dragging = false;
- public void mousePressed(MouseEvent evt)
- {
-
- selectedCheck = (MyCheckbox) evt.getSource();
-
- if (fr.featureLinks != null
- && fr.featureLinks.containsKey(selectedCheck.type))
- {
- if (evt.getX() > selectedCheck.stringWidth + 20)
- {
- evt.consume();
- }
- }
-
- }
-
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (((Component) evt.getSource()).getParent() != featurePanel)
dragging = true;
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (((Component) evt.getSource()).getParent() != featurePanel)
}
else
{
- comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
- + evt.getComponent().getLocation().y);
+ comp = featurePanel.getComponentAt(evt.getX(),
+ evt.getY() + evt.getComponent().getLocation().y);
}
if (comp != null && comp instanceof Checkbox)
}
}
- public void setUserColour(String feature, Object originalColour)
+ public void setUserColour(String feature, FeatureColourI originalColour)
{
- if (originalColour instanceof Color
- || originalColour instanceof GraduatedColor)
- {
- fr.setColour(feature, originalColour);
- }
- else
- {
- throw new Error(
- MessageManager
- .getString("error.implementation_error_unsupported_feature_colour_object"));
- }
+ fr.setColour(feature, originalColour);
refreshTable();
}
{
featurePanel.removeAll();
resetTable(false);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
MyCheckbox check = (MyCheckbox) evt.getSource();
{
this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
}
- if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
- {
- if (evt.getX() > check.stringWidth + 20)
- {
- evt.consume();
- String link = fr.featureLinks.get(check.type).toString();
- ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
- link.substring(0, link.indexOf("|")));
- }
- }
if (check.getParent() != featurePanel)
{
if (evt.getClickCount() > 1)
{
- Object fcol = fr.getFeatureStyle(check.type);
- if (fcol instanceof Color)
+ FeatureColourI fcol = fr.getFeatureStyle(check.type);
+ if (fcol.isSimpleColour())
{
- new UserDefinedColours(this, check.type, (Color) fcol);
+ new UserDefinedColours(this, check.type, fcol.getColour());
}
else
{
}
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- ap.seqPanel.seqCanvas.repaint();
-
+ ap.paintAlignment(true, true);
}
class MyCheckbox extends Checkbox
boolean hasLink;
- GraduatedColor gcol;
-
- Color col;
+ FeatureColourI col;
- public void updateColor(Object newcol)
+ public void updateColor(FeatureColourI newcol)
{
- if (newcol instanceof Color)
+ col = newcol;
+ if (col.isSimpleColour())
{
- col = (Color) newcol;
- gcol = null;
- }
- else if (newcol instanceof GraduatedColor)
- {
- gcol = (GraduatedColor) newcol;
- col = null;
- }
- else
- {
- throw new Error(
- MessageManager
- .getString("error.invalid_colour_for_mycheckbox"));
- }
- if (col != null)
- {
- setBackground(col);
+ setBackground(col.getColour());
}
else
{
String vlabel = type;
- if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (col.isAboveThreshold())
{
- vlabel += " "
- + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
- : "(<)");
+ vlabel += " (>)";
}
- if (gcol.isColourByLabel())
+ else if (col.isBelowThreshold())
+ {
+ vlabel += " (<)";
+ }
+ if (col.isColourByLabel())
{
setBackground(Color.white);
vlabel += " (by Label)";
}
else
{
- setBackground(gcol.getMinColor());
+ setBackground(col.getMinColour());
}
this.setLabel(vlabel);
}
}
public MyCheckbox(String type, boolean selected, boolean b,
- Object featureStyle)
+ FeatureColourI featureStyle)
{
this(type, selected, b);
updateColor(featureStyle);
}
+ @Override
public void paint(Graphics g)
{
Dimension d = getSize();
- if (gcol != null)
+ if (col != null)
{
- if (gcol.isColourByLabel())
+ if (col.isColourByLabel())
{
g.setColor(Color.white);
g.fillRect(d.width / 2, 0, d.width / 2, d.height);
*/
}
- else
+ else if (col.isGraduatedColour())
{
- Color maxCol = gcol.getMaxColor();
+ Color maxCol = col.getMaxColour();
g.setColor(maxCol);
g.fillRect(d.width / 2, 0, d.width / 2, d.height);
}
}
+ /**
+ * Hide columns containing (or not containing) a given feature type
+ *
+ * @param type
+ * @param columnsContaining
+ */
+ void hideFeatureColumns(final String type, boolean columnsContaining)
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+ false, false, type))
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(
+ !columnsContaining, false, false, type))
+ {
+ ap.alignFrame.viewport.hideSelectedColumns();
+ }
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff