/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
*/
package jalview.appletgui;
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;
-public class FeatureSettings
- extends Panel implements ItemListener,
- MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
+public class FeatureSettings extends Panel implements ItemListener,
+ MouseListener, MouseMotionListener, ActionListener,
+ AdjustmentListener
{
FeatureRenderer fr;
+
AlignmentPanel ap;
+
AlignViewport av;
+
Frame frame;
+
Panel groupPanel;
+
Panel featurePanel = new Panel();
+
ScrollPane scrollPane;
+
boolean alignmentHasFeatures = false;
+
Image linkImage;
+
Scrollbar transparency;
public FeatureSettings(final AlignmentPanel ap)
fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
transparency = new Scrollbar(Scrollbar.HORIZONTAL,
- 100 - (int) (fr.transparency * 100), 1, 1, 100);
+ 100 - (int) (fr.transparency * 100), 1, 1, 100);
if (fr.transparencySetter != null)
{
}
else
{
- tPanel.add(new Label("Transparency not available in this web browser"),
- BorderLayout.CENTER);
+ tPanel.add(
+ new Label("Transparency not available in this web browser"),
+ BorderLayout.CENTER);
}
lowerPanel.add(tPanel, BorderLayout.SOUTH);
if (groupPanel != null)
{
- groupPanel.setLayout(
- new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+ groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
+ 4));
groupPanel.validate();
add(groupPanel, BorderLayout.NORTH);
{
public void windowClosing(WindowEvent e)
{
- if (me.av.featureSettings==me)
+ if (me.av.featureSettings == me)
{
me.av.featureSettings = null;
me.ap = null;
me.av = null;
}
}
- }
- );
+ });
int height = featurePanel.getComponentCount() * 50 + 60;
height = Math.max(200, height);
height = Math.min(400, height);
int width = 300;
jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width,
- height);
+ height);
}
public void paint(Graphics g)
g.drawString("from Jalview / GFF features files)", 10, 60);
}
+ protected void popupSort(final MyCheckbox check, final Hashtable 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");
+ men.add(scr);
+ final FeatureSettings me = this;
+ scr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.sortByScore(new String[]
+ { type });
+ }
+
+ });
+ MenuItem dens = new MenuItem("Sort by Density");
+ dens.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.sortByDens(new String[]
+ { type });
+ }
+
+ });
+ men.add(dens);
+ if (minmax != null)
+ {
+ final Object typeMinMax = minmax.get(type);
+ /*
+ * final java.awt.CheckboxMenuItem chb = new
+ * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
+ * moment chb.setState(minmax.get(type) != null);
+ * chb.addActionListener(new ActionListener() {
+ *
+ * public void actionPerformed(ActionEvent e) {
+ * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
+ * null); } else { minmax.put(type, typeMinMax); } }
+ *
+ * }); men.add(chb);
+ */
+ if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+ {
+ // graduated colourschemes for those where minmax exists for the
+ // positional features
+ MenuItem mxcol = new MenuItem(
+ (typeCol instanceof Color) ? "Graduated Colour"
+ : "Single Colour");
+ men.add(mxcol);
+ mxcol.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ if (typeCol instanceof Color)
+ {
+ new FeatureColourChooser(me, type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(type));
+ }
+ else
+ {
+ new UserDefinedColours(me, check.type,
+ ((GraduatedColor) typeCol));
+ }
+ }
+
+ });
+ }
+ }
+ this.featurePanel.add(men);
+ men.show(this.featurePanel, x, y);
+ }
+
public void setTableData()
{
alignmentHasFeatures = fr.buildGroupHash();
if (alignmentHasFeatures)
{
rebuildGroups();
-
+
}
resetTable(false);
}
+
/**
* rebuilds the group panel
*/
if (groupPanel == null)
{
groupPanel = new Panel();
- } else {
+ }
+ else
+ {
rdrw = true;
groupPanel.removeAll();
}
-
+
Enumeration gps = fr.featureGroups.keys();
while (gps.hasMoreElements())
{
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))
- );
+ Checkbox check = new MyCheckbox(group, vis.booleanValue(),
+ (fr.featureLinks != null && fr.featureLinks
+ .containsKey(group)));
check.addMouseListener(this);
check.setFont(new Font("Serif", Font.BOLD, 12));
check.addItemListener(this);
}
}
- //This routine adds and removes checkboxes depending on
- //Group selection states
+ // This routine adds and removes checkboxes depending on
+ // Group selection states
void resetTable(boolean groupsChanged)
{
SequenceFeature[] tmpfeatures;
{
group = tmpfeatures[index].featureGroup;
- if (group == null || fr.featureGroups.get(group) == null ||
- ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+ if (group == null || fr.featureGroups.get(group) == null
+ || ((Boolean) fr.featureGroups.get(group)).booleanValue())
{
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
Component[] comps;
int cSize = featurePanel.getComponentCount();
- Checkbox check;
- //This will remove any checkboxes which shouldn't be
- //visible
+ MyCheckbox check;
+ // This will remove any checkboxes which shouldn't be
+ // visible
for (int i = 0; i < cSize; i++)
{
comps = featurePanel.getComponents();
- check = (Checkbox) comps[i];
- if (!visibleChecks.contains(check.getLabel()))
+ check = (MyCheckbox) comps[i];
+ if (!visibleChecks.contains(check.type))
{
featurePanel.remove(i);
cSize--;
if (fr.renderOrder != null)
{
- //First add the checks in the previous render order,
- //in case the window has been closed and reopened
+ // 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--)
{
String item = fr.renderOrder[ro];
addCheck(groupsChanged, en.nextElement().toString());
}
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1,
- 10, 5));
+ featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
+ 1, 10, 5));
featurePanel.validate();
if (scrollPane != null)
itemStateChanged(null);
}
+
/**
* update the checklist of feature types with the given type
- * @param groupsChanged true means if the type is not in the display list then it will be added and displayed
- * @param type feature type to be checked for in the list.
+ *
+ * @param groupsChanged
+ * true means if the type is not in the display list then it will be
+ * added and displayed
+ * @param type
+ * feature type to be checked for in the list.
*/
void addCheck(boolean groupsChanged, String type)
{
boolean addCheck;
Component[] comps = featurePanel.getComponents();
- Checkbox check;
+ MyCheckbox check;
addCheck = true;
for (int i = 0; i < featurePanel.getComponentCount(); i++)
{
- check = (Checkbox) comps[i];
- if (check.getLabel().equals(type))
+ check = (MyCheckbox) comps[i];
+ if (check.type.equals(type))
{
addCheck = false;
break;
selected = true;
}
- check = new MyCheckbox(type,
- selected,
- (fr.featureLinks != null &&
- fr.featureLinks.containsKey(type))
- );
+ check = new MyCheckbox(
+ type,
+ selected,
+ (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+ fr.getFeatureStyle(type));
check.addMouseListener(this);
check.addMouseMotionListener(this);
- check.setBackground(fr.getColour(type));
check.addItemListener(this);
- featurePanel.add(check);
+ if (groupsChanged)
+ {
+ // add at beginning of stack.
+ featurePanel.add(check, 0);
+ }
+ else
+ {
+ // add at end of stack.
+ featurePanel.add(check);
+ }
}
}
{
if (evt != null)
{
- //Is the source a top level featureGroup?
+ // Is the source a top level featureGroup?
Checkbox source = (Checkbox) evt.getSource();
if (fr.featureGroups.containsKey(source.getLabel()))
{
- fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
+ fr.featureGroups.put(source.getLabel(), new Boolean(source
+ .getState()));
ap.seqPanel.seqCanvas.repaint();
if (ap.overviewPanel != null)
{
int tmpSize = 0;
for (int i = 0; i < cSize; i++)
{
- Checkbox check = (Checkbox) comps[i];
- tmp[tmpSize][0] = check.getLabel();
- tmp[tmpSize][1] = fr.getColour(check.getLabel());
+ MyCheckbox check = (MyCheckbox) comps[i];
+ tmp[tmpSize][0] = check.type;
+ tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
tmp[tmpSize][2] = new Boolean(check.getState());
tmpSize++;
}
}
MyCheckbox selectedCheck;
+
boolean dragging = false;
public void mousePressed(MouseEvent evt)
selectedCheck = (MyCheckbox) evt.getSource();
if (fr.featureLinks != null
- && fr.featureLinks.containsKey(selectedCheck.getLabel())
- )
+ && fr.featureLinks.containsKey(selectedCheck.type))
{
if (evt.getX() > selectedCheck.stringWidth + 20)
{
public void mouseDragged(MouseEvent evt)
{
- if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+ if (((Component) evt.getSource()).getParent() != featurePanel)
{
return;
}
public void mouseReleased(MouseEvent evt)
{
- if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+ if (((Component) evt.getSource()).getParent() != featurePanel)
{
return;
}
if (height > featurePanel.getSize().height)
{
- comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1);
+ comp = featurePanel
+ .getComponent(featurePanel.getComponentCount() - 1);
}
else if (height < 0)
{
}
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)
target = (Checkbox) comp;
}
- if (selectedCheck != null
- && target != null
- && selectedCheck != target)
+ if (selectedCheck != null && target != null && selectedCheck != target)
{
int targetIndex = -1;
for (int i = 0; i < featurePanel.getComponentCount(); i++)
}
}
- public void setUserColour(String feature, Color col)
+ public void setUserColour(String feature, Object originalColour)
+ {
+ if (originalColour instanceof Color
+ || originalColour instanceof GraduatedColor)
+ {
+ fr.setColour(feature, originalColour);
+ }
+ else
+ {
+ throw new Error(
+ "Implementation error: Unsupported feature colour object.");
+ }
+ refreshTable();
+ }
+
+ public void refreshTable()
{
- fr.setColour(feature, col);
featurePanel.removeAll();
resetTable(false);
ap.paintAlignment(true);
}
public void mouseEntered(MouseEvent evt)
- {}
+ {
+ }
public void mouseExited(MouseEvent evt)
- {}
+ {
+ }
public void mouseClicked(MouseEvent evt)
{
MyCheckbox check = (MyCheckbox) evt.getSource();
-
- if (fr.featureLinks != null
- && fr.featureLinks.containsKey(check.getLabel()))
+ 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.getLabel()).toString();
- ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
- link.substring(0, link.indexOf("|")));
+ String link = fr.featureLinks.get(check.type).toString();
+ ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), link
+ .substring(0, link.indexOf("|")));
}
}
if (evt.getClickCount() > 1)
{
- new UserDefinedColours(this, check.getLabel(),
- fr.getColour(check.getLabel()));
+ Object fcol = fr.getFeatureStyle(check.type);
+ if (fcol instanceof Color)
+ {
+ new UserDefinedColours(this, check.type, (Color) fcol);
+ }
+ else
+ {
+ new FeatureColourChooser(this, check.type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(check.type));
+ }
}
}
public void mouseMoved(MouseEvent evt)
- {}
+ {
+ }
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);
+ fr.transparency = ((float) (100 - transparency.getValue()) / 100f);
ap.seqPanel.seqCanvas.repaint();
}
- class MyCheckbox
- extends Checkbox
+ class MyCheckbox extends Checkbox
{
+ public String type;
+
public int stringWidth;
+
boolean hasLink;
+
+ GraduatedColor gcol;
+
+ Color col;
+
+ public void updateColor(Object newcol)
+ {
+ if (newcol instanceof Color)
+ {
+ 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);
+ }
+ else
+ {
+ String vlabel = type;
+ if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ vlabel += " "
+ + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
+ : "(<)");
+ }
+ if (gcol.isColourByLabel())
+ {
+ setBackground(Color.white);
+ vlabel += " (by Label)";
+ }
+ else
+ {
+ setBackground(gcol.getMinColor());
+ }
+ this.setLabel(vlabel);
+ }
+ repaint();
+ }
+
public MyCheckbox(String label, boolean checked, boolean haslink)
{
super(label, checked);
-
+ type = label;
FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
stringWidth = fm.stringWidth(label);
this.hasLink = haslink;
}
+ public MyCheckbox(String type, boolean selected, boolean b,
+ Object featureStyle)
+ {
+ this(type, selected, b);
+ updateColor(featureStyle);
+ }
+
public void paint(Graphics g)
{
+ Dimension d = getSize();
+ if (gcol != null)
+ {
+ if (gcol.isColourByLabel())
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ /*
+ * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
+ * g.setFont(f);
+ *
+ * // g.setFont(g.getFont().deriveFont( //
+ * AffineTransform.getScaleInstance( //
+ * width/g.getFontMetrics().stringWidth("Label"), //
+ * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
+ * width/2, 0);
+ */
+
+ }
+ else
+ {
+ Color maxCol = gcol.getMaxColor();
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+
+ }
+ }
+
if (hasLink)
{
- g.drawImage(linkImage, stringWidth + 25, (
- getSize().height - linkImage.getHeight(this)) / 2,
- this);
+ g.drawImage(linkImage, stringWidth + 25,
+ (getSize().height - linkImage.getHeight(this)) / 2, this);
}
}
}
+
+ 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