/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Image;
+import java.awt.Label;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.ScrollPane;
+import java.awt.Scrollbar;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener
+ AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
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)
- {
- transparency.addAdjustmentListener(this);
- }
- else
- {
- transparency.setEnabled(false);
- }
+ transparency.addAdjustmentListener(this);
java.net.URL url = getClass().getResource("/images/link.gif");
if (url != null)
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();
+ discoverAllFeatureData();
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)
- {
- 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);
if (groupPanel != null)
{
- groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
- 4));
+ 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);
final FeatureSettings me = this;
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
if (me.av.featureSettings == me)
height = Math.max(200, height);
height = Math.min(400, height);
int width = 300;
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width,
- height);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ width, height);
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.black);
- g.drawString("No Features added to this alignment!!", 10, 20);
- g.drawString("(Features can be added from searches or", 10, 40);
- g.drawString("from Jalview / GFF features files)", 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("Settings for " + type);
- java.awt.MenuItem scr = new MenuItem("Sort by Score");
+ 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);
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.sortByScore(new String[]
- { type });
+ me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
+ .asList(new String[] { type }));
}
});
- MenuItem dens = new MenuItem("Sort by Density");
+ MenuItem dens = new MenuItem(
+ MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.sortByDens(new String[]
- { type });
+ me.ap.alignFrame.avc.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);
}
- public void setTableData()
+ @Override
+ public void discoverAllFeatureData()
{
- alignmentHasFeatures = fr.buildGroupHash();
- if (alignmentHasFeatures)
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
{
rebuildGroups();
rdrw = true;
groupPanel.removeAll();
}
-
- Enumeration gps = fr.featureGroups.keys();
- while (gps.hasMoreElements())
+ // TODO: JAL-964 - smoothly incorporate new group entries if panel already
+ // displayed and new groups present
+ for (String group : fr.getFeatureGroups())
{
- String group = (String) gps.nextElement();
- Boolean vis = (Boolean) fr.featureGroups.get(group);
- Checkbox check = new MyCheckbox(group, vis.booleanValue(),
- (fr.featureLinks != null && fr.featureLinks
- .containsKey(group)));
+ boolean vis = fr.checkGroupVisibility(group, false);
+ Checkbox check = new MyCheckbox(group, vis, false);
check.addMouseListener(this);
check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(this);
+ check.addItemListener(groupItemListener);
+ // note - visibility seems to correlate with displayed. ???wtf ??
+ check.setVisible(vis);
groupPanel.add(check);
}
if (rdrw)
{
SequenceFeature[] tmpfeatures;
String group = null, type;
- Vector visibleChecks = new Vector();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ Vector<String> visibleChecks = new Vector<String>();
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
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))
{
// now add checkboxes which should be visible,
// if they have not already been added
- Enumeration en = visibleChecks.elements();
+ Enumeration<String> en = visibleChecks.elements();
while (en.hasMoreElements())
{
if (addCheck)
{
boolean selected = false;
- if (groupsChanged || av.featuresDisplayed.containsKey(type))
+ if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
{
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++)
selectionChanged();
}
- public void itemStateChanged(ItemEvent evt)
+ private ItemListener groupItemListener = new ItemListener()
{
- if (evt != null)
+ @Override
+ public void itemStateChanged(ItemEvent evt)
{
- // Is the source a top level featureGroup?
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;
+ };
+ };
+
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
selectionChanged();
}
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)
}
}
- 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(
- "Implementation error: Unsupported feature colour object.");
- }
+ fr.setColour(feature, originalColour);
refreshTable();
}
ap.paintAlignment(true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
MyCheckbox check = (MyCheckbox) evt.getSource();
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
{
- this.popupSort(check, fr.minmax, 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("|")));
- }
+ this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
}
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.transparency = ((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
ap.seqPanel.seqCanvas.repaint();
}
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("Invalid color 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);
}
}
- protected void sortByDens(String[] typ)
- {
- sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
- }
-
- private String[] getDisplayedFeatureTypes()
+ /**
+ * Hide columns containing (or not containing) a given feature type
+ *
+ * @param type
+ * @param columnsContaining
+ */
+ void hideFeatureColumns(final String type, boolean columnsContaining)
{
- String[] typ = null;
- if (fr != null)
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+ false, false, type))
{
- synchronized (fr.renderOrder)
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(
+ !columnsContaining, false, false, type))
{
- 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;
- }
- }
+ ap.alignFrame.viewport.hideSelectedColumns();
}
}
- return typ;
}
- protected void sortBy(String[] typ, String methodText, final String method)
+ @Override
+ public void mousePressed(MouseEvent e)
{
- 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);
+ // TODO Auto-generated method stub
}
- protected void sortByScore(String[] typ)
- {
- sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
- }
-
}
git://source.jalview.org / jalview.git / blobdiff