X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=d7f05dcc3e1bc1e4ce2c019eaa3ce17efde35e17;hb=ae6c88485c83b2ca89e64c9daf2e925953a6f87a;hp=22800ea30f07175787f964904cb3d3e1ac6ef560;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
old mode 100755
new mode 100644
index 22800ea..d7f05dc
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,26 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.io.*;
import java.util.*;
-
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
import java.beans.PropertyChangeEvent;
@@ -31,10 +31,14 @@ import javax.swing.event.*;
import javax.swing.table.*;
import jalview.analysis.AlignmentSorter;
+import jalview.bin.Cache;
import jalview.commands.OrderCommand;
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
public class FeatureSettings extends JPanel
{
@@ -62,7 +66,7 @@ public class FeatureSettings extends JPanel
JSlider transparency = new JSlider();
- JPanel transPanel = new JPanel(new FlowLayout());
+ JPanel transPanel = new JPanel(new GridLayout(1, 2));
public FeatureSettings(AlignFrame af)
{
@@ -84,8 +88,10 @@ public class FeatureSettings extends JPanel
table.setFont(new Font("Verdana", Font.PLAIN, 12));
table.setDefaultRenderer(Color.class, new ColorRenderer());
- table.setDefaultEditor(Color.class, new ColorEditor());
+ table.setDefaultEditor(Color.class, new ColorEditor(this));
+ table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this));
+ table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer());
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.addMouseListener(new MouseAdapter()
@@ -93,10 +99,17 @@ public class FeatureSettings extends JPanel
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
+ {
+ popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
+ table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
+ evt.getY());
+ }
+ else if (evt.getClickCount() == 2)
{
- popupSort((String) table.getValueAt(selectedRow, 0), fr.minmax,
- evt.getX(), evt.getY());
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(
+ evt.isShiftDown(),
+ (String) table.getValueAt(selectedRow, 0));
}
}
});
@@ -128,7 +141,7 @@ public class FeatureSettings extends JPanel
scrollPane.setViewportView(table);
- dassourceBrowser = new DasSourceBrowser();
+ dassourceBrowser = new DasSourceBrowser(this);
dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
if (af.getViewport().featuresDisplayed == null
@@ -157,24 +170,32 @@ public class FeatureSettings extends JPanel
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
- frame
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- fr.removePropertyChangeListener(change);
- };
- });
+ if (new jalview.util.Platform().isAMac())
+ {
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 475, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 400, 450);
+ }
+
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ dassourceBrowser.fs = null;
+ };
+ });
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
- protected void popupSort(final String type, final Hashtable minmax,
- int x, int y)
+ protected void popupSort(final int selectedRow, final String type,
+ final Object typeCol, final Hashtable minmax, int x, int y)
{
- JPopupMenu men = new JPopupMenu("Settings for " + type);
- JMenuItem scr = new JMenuItem("Sort by Score");
+ JPopupMenu men = new JPopupMenu(MessageManager.formatMessage("label.settings_for_param", new String[]{type}));
+ JMenuItem scr = new JMenuItem(MessageManager.getString("label.sort_by_score"));
men.add(scr);
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
@@ -187,7 +208,7 @@ public class FeatureSettings extends JPanel
}
});
- JMenuItem dens = new JMenuItem("Sort by Density");
+ JMenuItem dens = new JMenuItem(MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
@@ -202,43 +223,102 @@ public class FeatureSettings extends JPanel
if (minmax != null)
{
final Object typeMinMax = minmax.get(type);
- final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height");
- // this is broken at the moment
- chb.setSelected(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);
+ /*
+ * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
+ * this is broken at the moment and isn't that useful anyway!
+ * chb.setSelected(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
- JMenuItem mxcol = new JMenuItem("Min Max Colour");
+ // if (table.getValueAt(row, column));
+ // graduated colourschemes for those where minmax exists for the
+ // positional features
+ final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
+ "Graduated Colour");
+ mxcol.setSelected(!(typeCol instanceof Color));
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
{
+ JColorChooser colorChooser;
public void actionPerformed(ActionEvent e)
{
- new FeatureColourChooser(me, type);
+ if (e.getSource() == mxcol)
+ {
+ if (typeCol instanceof Color)
+ {
+ FeatureColourChooser fc = new FeatureColourChooser(me.fr,
+ type);
+ fc.addActionListener(this);
+ }
+ else
+ {
+ // bring up simple color chooser
+ colorChooser = new JColorChooser();
+ JDialog dialog = JColorChooser.createDialog(me,
+ "Select new Colour", true, // modal
+ colorChooser, this, // OK button handler
+ null); // no CANCEL button handler
+ colorChooser.setColor(((GraduatedColor) typeCol)
+ .getMaxColor());
+ dialog.setVisible(true);
+ }
+ }
+ else
+ {
+ if (e.getSource() instanceof FeatureColourChooser)
+ {
+ FeatureColourChooser fc = (FeatureColourChooser) e
+ .getSource();
+ table.setValueAt(fc.getLastColour(), selectedRow, 1);
+ table.validate();
+ }
+ else
+ {
+ // probably the color chooser!
+ table.setValueAt(colorChooser.getColor(), selectedRow, 1);
+ table.validate();
+ me.updateFeatureRenderer(
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
+ }
+ }
}
});
}
}
+ JMenuItem selCols = new JMenuItem(MessageManager.getString("label.select_columns_containing"));
+ selCols.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, type);
+ }
+ });
+ JMenuItem clearCols = new JMenuItem(MessageManager.getString("label.select_columns_not_containing"));
+ clearCols.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, type);
+ }
+ });
+ men.add(selCols);
+ men.add(clearCols);
men.show(table, x, y);
}
@@ -262,15 +342,15 @@ public class FeatureSettings extends JPanel
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
- .getSequenceFeatures() == null)
+ if (af.getViewport().getAlignment().getSequenceAt(i)
+ .getDatasetSequence().getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
int index = 0;
@@ -355,8 +435,8 @@ public class FeatureSettings extends JPanel
{
public void itemStateChanged(ItemEvent evt)
{
- fr.featureGroups.put(check.getText(), new Boolean(check
- .isSelected()));
+ fr.featureGroups.put(check.getText(),
+ new Boolean(check.isSelected()));
af.alignPanel.seqPanel.seqCanvas.repaint();
if (af.alignPanel.overviewPanel != null)
{
@@ -391,10 +471,10 @@ public class FeatureSettings extends JPanel
// Find out which features should be visible depending on which groups
// are selected / deselected
// and recompute average width ordering
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
if (tmpfeatures == null)
{
@@ -469,9 +549,9 @@ public class FeatureSettings extends JPanel
}
data[dataIndex][0] = type;
- data[dataIndex][1] = fr.getColour(type);
- data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed
- .containsKey(type));
+ data[dataIndex][1] = fr.getFeatureStyle(type);
+ data[dataIndex][2] = new Boolean(
+ af.getViewport().featuresDisplayed.containsKey(type));
dataIndex++;
visibleChecks.removeElement(type);
}
@@ -485,7 +565,7 @@ public class FeatureSettings extends JPanel
type = visibleChecks.elementAt(i).toString();
data[dataIndex][0] = type;
- data[dataIndex][1] = fr.getColour(type);
+ data[dataIndex][1] = fr.getFeatureStyle(type);
if (data[dataIndex][1] == null)
{
// "Colour has been updated in another view!!"
@@ -500,7 +580,10 @@ public class FeatureSettings extends JPanel
if (originalData == null)
{
originalData = new Object[data.length][3];
- System.arraycopy(data, 0, originalData, 0, data.length);
+ for (int i = 0; i < data.length; i++)
+ {
+ System.arraycopy(data[i], 0, originalData[i], 0, 3);
+ }
}
table.setModel(new FeatureTableModel(data));
@@ -542,13 +625,13 @@ public class FeatureSettings extends JPanel
void load()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "fc" }, new String[]
+ { "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Load Feature Colours");
- chooser.setToolTipText("Load");
+ chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
@@ -561,14 +644,65 @@ public class FeatureSettings extends JPanel
InputStreamReader in = new InputStreamReader(new FileInputStream(
file), "UTF-8");
- jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+ jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
+ jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs
+ .unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
String name;
- fr.setColour(name = jucs.getColour(i).getName(), new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
+ if (newcol.hasMax())
+ {
+ Color mincol = null, maxcol = null;
+ try
+ {
+ mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
+ maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
+
+ } catch (Exception e)
+ {
+ Cache.log.warn("Couldn't parse out graduated feature color.",
+ e);
+ }
+ GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+ newcol.getMin(), newcol.getMax());
+ if (newcol.hasAutoScale())
+ {
+ gcol.setAutoScaled(newcol.getAutoScale());
+ }
+ if (newcol.hasColourByLabel())
+ {
+ gcol.setColourByLabel(newcol.getColourByLabel());
+ }
+ if (newcol.hasThreshold())
+ {
+ gcol.setThresh(newcol.getThreshold());
+ gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
+ }
+ if (newcol.getThreshType().length() > 0)
+ {
+ String ttyp = newcol.getThreshType();
+ if (ttyp.equalsIgnoreCase("NONE"))
+ {
+ gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
+ }
+ if (ttyp.equalsIgnoreCase("ABOVE"))
+ {
+ gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ }
+ if (ttyp.equalsIgnoreCase("BELOW"))
+ {
+ gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ }
+ }
+ fr.setColour(name = newcol.getName(), gcol);
+ }
+ else
+ {
+ fr.setColour(name = jucs.getColour(i).getName(), new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ }
fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
}
if (table != null)
@@ -589,44 +723,70 @@ public class FeatureSettings extends JPanel
void save()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "fc" }, new String[]
+ { "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Save Feature Colour Scheme");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+ jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
ucs.setSchemeName("Sequence Features");
try
{
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
- Enumeration e = fr.featureColours.keys();
+ Iterator e = fr.featureColours.keySet().iterator();
float[] sortOrder = new float[fr.featureColours.size()];
String[] sortTypes = new String[fr.featureColours.size()];
int i = 0;
- while (e.hasMoreElements())
+ while (e.hasNext())
{
- sortTypes[i] = e.nextElement().toString();
+ sortTypes[i] = e.next().toString();
sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
jalview.util.QuickSort.sort(sortOrder, sortTypes);
sortOrder = null;
+ Object fcol;
+ GraduatedColor gcol;
for (i = 0; i < sortTypes.length; i++)
{
- jalview.binding.Colour col = new jalview.binding.Colour();
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(sortTypes[i]);
col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
.getName())));
+ fcol = fr.getFeatureStyle(sortTypes[i]);
+ if (fcol instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) fcol;
+ col.setMin(gcol.getMin());
+ col.setMax(gcol.getMax());
+ col.setMinRGB(jalview.util.Format.getHexString(gcol
+ .getMinColor()));
+ col.setAutoScale(gcol.isAutoScale());
+ col.setThreshold(gcol.getThresh());
+ col.setColourByLabel(gcol.isColourByLabel());
+ switch (gcol.getThreshType())
+ {
+ case AnnotationColourGradient.NO_THRESHOLD:
+ col.setThreshType("NONE");
+ break;
+ case AnnotationColourGradient.ABOVE_THRESHOLD:
+ col.setThreshType("ABOVE");
+ break;
+ case AnnotationColourGradient.BELOW_THRESHOLD:
+ col.setThreshType("BELOW");
+ break;
+ }
+ }
ucs.addColour(col);
}
ucs.marshal(out);
@@ -765,7 +925,7 @@ public class FeatureSettings extends JPanel
JButton sortByDens = new JButton();
- JPanel transbuttons = new JPanel(new BorderLayout());
+ JPanel transbuttons = new JPanel(new GridLayout(4, 1));
private void jbInit() throws Exception
{
@@ -773,8 +933,8 @@ public class FeatureSettings extends JPanel
settingsPane.setLayout(borderLayout2);
dasSettingsPane.setLayout(borderLayout3);
bigPanel.setLayout(borderLayout4);
- invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- invert.setText("Invert Selection");
+ invert.setFont(JvSwingUtils.getLabelFont());
+ invert.setText(MessageManager.getString("label.invert_selection"));
invert.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -782,8 +942,8 @@ public class FeatureSettings extends JPanel
invertSelection();
}
});
- optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- optimizeOrder.setText("Optimise Order");
+ optimizeOrder.setFont(JvSwingUtils.getLabelFont());
+ optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
optimizeOrder.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -791,8 +951,8 @@ public class FeatureSettings extends JPanel
orderByAvWidth();
}
});
- sortByScore.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- sortByScore.setText("Seq sort by Score");
+ sortByScore.setFont(JvSwingUtils.getLabelFont());
+ sortByScore.setText(MessageManager.getString("label.seq_sort_by_score"));
sortByScore.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -800,8 +960,8 @@ public class FeatureSettings extends JPanel
sortByScore(null);
}
});
- sortByDens.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- sortByDens.setText("Seq Sort by density");
+ sortByDens.setFont(JvSwingUtils.getLabelFont());
+ sortByDens.setText(MessageManager.getString("label.sequence_sort_by_density"));
sortByDens.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -809,8 +969,8 @@ public class FeatureSettings extends JPanel
sortByDens(null);
}
});
- cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- cancel.setText("Cancel");
+ cancel.setFont(JvSwingUtils.getLabelFont());
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -819,8 +979,8 @@ public class FeatureSettings extends JPanel
close();
}
});
- ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- ok.setText("OK");
+ ok.setFont(JvSwingUtils.getLabelFont());
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -828,8 +988,8 @@ public class FeatureSettings extends JPanel
close();
}
});
- loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- loadColours.setText("Load Colours");
+ loadColours.setFont(JvSwingUtils.getLabelFont());
+ loadColours.setText(MessageManager.getString("label.load_colours"));
loadColours.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -837,8 +997,8 @@ public class FeatureSettings extends JPanel
load();
}
});
- saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- saveColours.setText("Save Colours");
+ saveColours.setFont(JvSwingUtils.getLabelFont());
+ saveColours.setText(MessageManager.getString("label.save_colours"));
saveColours.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -856,7 +1016,7 @@ public class FeatureSettings extends JPanel
});
transparency.setMaximum(70);
- fetchDAS.setText("Fetch DAS Features");
+ fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
fetchDAS.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -864,7 +1024,7 @@ public class FeatureSettings extends JPanel
fetchDAS_actionPerformed(e);
}
});
- saveDAS.setText("Save as default");
+ saveDAS.setText(MessageManager.getString("action.save_as_default"));
saveDAS.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -875,7 +1035,7 @@ public class FeatureSettings extends JPanel
dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
dasSettingsPane.setBorder(null);
cancelDAS.setEnabled(false);
- cancelDAS.setText("Cancel Fetch");
+ cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
cancelDAS.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -887,16 +1047,16 @@ public class FeatureSettings extends JPanel
tabbedPane.addTab("Feature Settings", settingsPane);
tabbedPane.addTab("DAS Settings", dasSettingsPane);
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
+ transbuttons.add(optimizeOrder);
+ transbuttons.add(invert);
+ transbuttons.add(sortByScore);
+ transbuttons.add(sortByDens);
transPanel.add(transparency);
- transbuttons.add(invert, java.awt.BorderLayout.NORTH);
- transbuttons.add(optimizeOrder, java.awt.BorderLayout.SOUTH);
transPanel.add(transbuttons);
buttonPanel.add(ok);
buttonPanel.add(cancel);
buttonPanel.add(loadColours);
buttonPanel.add(saveColours);
- buttonPanel.add(sortByScore);
- buttonPanel.add(sortByDens);
bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
dasButtonPanel.add(fetchDAS);
@@ -921,18 +1081,30 @@ public class FeatureSettings extends JPanel
gps = getDisplayedFeatureGroups();
if (typ != null)
{
+ ArrayList types = new ArrayList();
for (int i = 0; i < typ.length; i++)
{
- System.err.println("Sorting on Types:" + typ[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++)
{
- System.err.println("Sorting on groups:" + gps[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();
@@ -991,13 +1163,13 @@ public class FeatureSettings extends JPanel
if (fr.featureGroups != null)
{
- Enumeration en = fr.featureGroups.keys();
+ Iterator en = fr.featureGroups.keySet().iterator();
gps = new String[fr.featureColours.size()];
int g = 0;
boolean valid = false;
- while (en.hasMoreElements())
+ while (en.hasNext())
{
- String gp = (String) en.nextElement();
+ String gp = (String) en.next();
Boolean on = (Boolean) fr.featureGroups.get(gp);
if (on != null && on.booleanValue())
{
@@ -1022,6 +1194,7 @@ public class FeatureSettings extends JPanel
{
fetchDAS.setEnabled(false);
cancelDAS.setEnabled(true);
+ dassourceBrowser.setGuiEnabled(false);
Vector selectedSources = dassourceBrowser.getSelectedSources();
doDasFeatureFetch(selectedSources, true, true);
}
@@ -1033,7 +1206,7 @@ public class FeatureSettings extends JPanel
* @param checkDbRefs
* @param promptFetchDbRefs
*/
- private void doDasFeatureFetch(Vector selectedSources,
+ private void doDasFeatureFetch(List selectedSources,
boolean checkDbRefs, boolean promptFetchDbRefs)
{
SequenceI[] dataset, seqs;
@@ -1078,12 +1251,12 @@ public class FeatureSettings extends JPanel
* nicknames in sources
*
* @param sources
- * Vector of Strings to resolve to DAS source nicknames.
+ * Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
- public Vector resolveSourceNicknames(Vector sources)
+ public List resolveSourceNicknames(Vector sources)
{
- return dassourceBrowser.resolveSourceNicknames(sources);
+ return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
}
/**
@@ -1102,29 +1275,41 @@ public class FeatureSettings extends JPanel
* features from the named sources (rather than any turned on by default)
*
* @param sources
+ * @param block
+ * if true then runs in same thread, otherwise passes to the Swing
+ * executor
*/
- public void fetchDasFeatures(Vector sources)
+ public void fetchDasFeatures(Vector sources, boolean block)
{
initDasSources();
- Vector resolved = resolveSourceNicknames(sources);
+ List resolved = dassourceBrowser.sourceRegistry
+ .resolveSourceNicknames(sources);
if (resolved.size() == 0)
{
resolved = dassourceBrowser.getSelectedSources();
}
if (resolved.size() > 0)
{
- final Vector dassources = resolved;
- SwingUtilities.invokeLater(new Runnable()
+ final List dassources = resolved;
+ fetchDAS.setEnabled(false);
+ // cancelDAS.setEnabled(true); doDasFetch does this.
+ Runnable fetcher = new Runnable()
{
public void run()
{
- fetchDAS.setEnabled(false);
- cancelDAS.setEnabled(true);
doDasFeatureFetch(dassources, true, false);
}
- });
+ };
+ if (block)
+ {
+ fetcher.run();
+ }
+ else
+ {
+ SwingUtilities.invokeLater(fetcher);
+ }
}
}
@@ -1138,6 +1323,8 @@ public class FeatureSettings extends JPanel
{
fetchDAS.setEnabled(true);
cancelDAS.setEnabled(false);
+ dassourceBrowser.setGuiEnabled(true);
+
}
public void cancelDAS_actionPerformed(ActionEvent e)
@@ -1146,17 +1333,15 @@ public class FeatureSettings extends JPanel
{
dasFeatureFetcher.cancel();
}
- fetchDAS.setEnabled(true);
- cancelDAS.setEnabled(false);
+ complete();
}
public void noDasSourceActive()
{
complete();
JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "No das sources were selected.\n"
- + "Please select some sources and\n" + " try again.",
- "No Sources Selected", JOptionPane.DEFAULT_OPTION,
+ MessageManager.getString("label.no_das_sources_selected_warn"),
+ MessageManager.getString("label.no_das_sources_selected_title"), JOptionPane.DEFAULT_OPTION,
JOptionPane.INFORMATION_MESSAGE);
}
@@ -1235,34 +1420,43 @@ public class FeatureSettings extends JPanel
javax.swing.border.Border selectedBorder = null;
+ final String baseTT = "Click to edit, right/apple click for menu.";
+
public ColorRenderer()
{
setOpaque(true); // MUST do this for background to show up.
+ setHorizontalTextPosition(SwingConstants.CENTER);
+ setVerticalTextPosition(SwingConstants.CENTER);
}
public Component getTableCellRendererComponent(JTable table,
Object color, boolean isSelected, boolean hasFocus, int row,
int column)
{
+ // JLabel comp = new JLabel();
+ // comp.
+ setOpaque(true);
+ // comp.
+ // setBounds(getBounds());
Color newColor;
- color = fr.featureColours.get((String) table.getModel().getValueAt(
- row, 0));
+ setToolTipText(baseTT);
+ setBackground(table.getBackground());
if (color instanceof GraduatedColor)
{
- newColor = ((GraduatedColor) color).getMaxColor();
- Color minCol = ((GraduatedColor) color).getMinColor();;
- setBackground(newColor);
- setToolTipText("RGB value: Max (" + newColor.getRed() + ", "
- + newColor.getGreen() + ", " + newColor.getBlue()
- + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
- + ", " + minCol.getBlue() + ")");
+ Rectangle cr = table.getCellRect(row, column, false);
+ FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color,
+ (int) cr.getWidth(), (int) cr.getHeight());
+
}
else
{
+ this.setText("");
+ this.setIcon(null);
newColor = (Color) color;
+ // comp.
setBackground(newColor);
- setToolTipText("RGB value: " + newColor.getRed() + ", "
- + newColor.getGreen() + ", " + newColor.getBlue());
+ // comp.setToolTipText("RGB value: " + newColor.getRed() + ", "
+ // + newColor.getGreen() + ", " + newColor.getBlue());
}
if (isSelected)
{
@@ -1271,6 +1465,7 @@ public class FeatureSettings extends JPanel
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
table.getSelectionBackground());
}
+ // comp.
setBorder(selectedBorder);
}
else
@@ -1280,17 +1475,182 @@ public class FeatureSettings extends JPanel
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
table.getBackground());
}
+ // comp.
setBorder(unselectedBorder);
}
return this;
}
}
+
+ /**
+ * update comp using rendering settings from gcol
+ *
+ * @param comp
+ * @param gcol
+ */
+ public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol)
+ {
+ int w = comp.getWidth(), h = comp.getHeight();
+ if (w < 20)
+ {
+ w = (int) comp.getPreferredSize().getWidth();
+ h = (int) comp.getPreferredSize().getHeight();
+ if (w < 20)
+ {
+ w = 80;
+ h = 12;
+ }
+ }
+ renderGraduatedColor(comp, gcol, w, h);
+ }
+
+ public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol,
+ int w, int h)
+ {
+ boolean thr = false;
+ String tt = "";
+ String tx = "";
+ if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
+ thr = true;
+ tx += ">";
+ tt += "Thresholded (Above " + gcol.getThresh() + ") ";
+ }
+ if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+ {
+ thr = true;
+ tx += "<";
+ tt += "Thresholded (Below " + gcol.getThresh() + ") ";
+ }
+ if (gcol.isColourByLabel())
+ {
+ tt = "Coloured by label text. " + tt;
+ if (thr)
+ {
+ tx += " ";
+ }
+ tx += "Label";
+ comp.setIcon(null);
+ }
+ else
+ {
+ Color newColor = gcol.getMaxColor();
+ comp.setBackground(newColor);
+ // System.err.println("Width is " + w / 2);
+ Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
+ comp.setIcon(ficon);
+ // tt+="RGB value: Max (" + newColor.getRed() + ", "
+ // + newColor.getGreen() + ", " + newColor.getBlue()
+ // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+ // + ", " + minCol.getBlue() + ")");
+ }
+ comp.setHorizontalAlignment(SwingConstants.CENTER);
+ comp.setText(tx);
+ if (tt.length() > 0)
+ {
+ if (comp.getToolTipText() == null)
+ {
+ comp.setToolTipText(tt);
+ }
+ else
+ {
+ comp.setToolTipText(tt + " " + comp.getToolTipText());
+ }
+ }
+ }
+}
+
+class FeatureIcon implements Icon
+{
+ GraduatedColor gcol;
+
+ Color backg;
+
+ boolean midspace = false;
+
+ int width = 50, height = 20;
+
+ int s1, e1; // start and end of midpoint band for thresholded symbol
+
+ Color mpcolour = Color.white;
+
+ FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace)
+ {
+ gcol = gfc;
+ backg = bg;
+ width = w;
+ height = h;
+ midspace = mspace;
+ if (midspace)
+ {
+ s1 = width / 3;
+ e1 = s1 * 2;
+ }
+ else
+ {
+ s1 = width / 2;
+ e1 = s1;
+ }
+ }
+
+ public int getIconWidth()
+ {
+ return width;
+ }
+
+ public int getIconHeight()
+ {
+ return height;
+ }
+
+ public void paintIcon(Component c, Graphics g, int x, int y)
+ {
+
+ if (gcol.isColourByLabel())
+ {
+ g.setColor(backg);
+ g.fillRect(0, 0, width, height);
+ // need an icon here.
+ g.setColor(gcol.getMaxColor());
+
+ g.setFont(new Font("Verdana", Font.PLAIN, 9));
+
+ // g.setFont(g.getFont().deriveFont(
+ // AffineTransform.getScaleInstance(
+ // width/g.getFontMetrics().stringWidth("Label"),
+ // height/g.getFontMetrics().getHeight())));
+
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
+
+ }
+ else
+ {
+ Color minCol = gcol.getMinColor();
+ g.setColor(minCol);
+ g.fillRect(0, 0, s1, height);
+ if (midspace)
+ {
+ g.setColor(Color.white);
+ g.fillRect(s1, 0, e1 - s1, height);
+ }
+ g.setColor(gcol.getMaxColor());
+ g.fillRect(0, e1, width - e1, height);
+ }
+ }
}
class ColorEditor extends AbstractCellEditor implements TableCellEditor,
ActionListener
{
+ FeatureSettings me;
+
+ GraduatedColor currentGColor;
+
+ FeatureColourChooser chooser;
+
+ String type;
+
Color currentColor;
JButton button;
@@ -1301,8 +1661,11 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
protected static final String EDIT = "edit";
- public ColorEditor()
+ int selectedRow = 0;
+
+ public ColorEditor(FeatureSettings me)
{
+ this.me = me;
// Set up the editor (from the table's point of view),
// which is a button.
// This button brings up the color chooser dialog,
@@ -1328,23 +1691,50 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
{
// The user has clicked the cell, so
// bring up the dialog.
- button.setBackground(currentColor);
- colorChooser.setColor(currentColor);
- dialog.setVisible(true);
-
+ if (currentColor != null)
+ {
+ // bring up simple color chooser
+ button.setBackground(currentColor);
+ colorChooser.setColor(currentColor);
+ dialog.setVisible(true);
+ }
+ else
+ {
+ // bring up graduated chooser.
+ chooser = new FeatureColourChooser(me.fr, type);
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ chooser.addActionListener(this);
+ }
// Make the renderer reappear.
fireEditingStopped();
}
else
{ // User pressed dialog's "OK" button.
- currentColor = colorChooser.getColor();
+ if (currentColor != null)
+ {
+ currentColor = colorChooser.getColor();
+ }
+ else
+ {
+ // class cast exceptions may be raised if the chooser created on a
+ // non-graduated color
+ currentGColor = (GraduatedColor) chooser.getLastColour();
+ }
+ me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
+ fireEditingStopped();
+ me.table.validate();
}
}
// Implement the one CellEditor method that AbstractCellEditor doesn't.
public Object getCellEditorValue()
{
+ if (currentColor == null)
+ {
+ return currentGColor;
+ }
return currentColor;
}
@@ -1352,7 +1742,29 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
public Component getTableCellEditorComponent(JTable table, Object value,
boolean isSelected, int row, int column)
{
- currentColor = (Color) value;
+ currentGColor = null;
+ currentColor = null;
+ this.selectedRow = row;
+ type = me.table.getValueAt(row, 0).toString();
+ button.setOpaque(true);
+ button.setBackground(me.getBackground());
+ if (value instanceof GraduatedColor)
+ {
+ currentGColor = (GraduatedColor) value;
+ JLabel btn = new JLabel();
+ btn.setSize(button.getSize());
+ FeatureSettings.renderGraduatedColor(btn, currentGColor);
+ button.setBackground(btn.getBackground());
+ button.setIcon(btn.getIcon());
+ button.setText(btn.getText());
+ }
+ else
+ {
+ button.setText("");
+ button.setIcon(null);
+ currentColor = (Color) value;
+ button.setBackground(currentColor);
+ }
return button;
}
}