X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=0f14bed5c85faf55daab3438968de886fbafc5c8;hb=e775f1627590b62ccad7cc5104667d347079497b;hp=8c156624c3094166f1210b1b2b3f541e4ed3fcc7;hpb=c1d578127a42ebd8535c3135241e9b0da789d584;p=jalview.git
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
old mode 100755
new mode 100644
index 8c15662..0f14bed
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,43 +1,95 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 .
+ * 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.awt.*;
-import java.awt.event.*;
-import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-
-import javax.swing.*;
-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.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Help.HelpId;
+import jalview.io.JalviewFileChooser;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import javax.help.HelpSetException;
+import javax.swing.AbstractCellEditor;
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JDialog;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JSlider;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
public class FeatureSettings extends JPanel
{
@@ -82,7 +134,19 @@ public class FeatureSettings extends JPanel
ex.printStackTrace();
}
- table = new JTable();
+ table = new JTable() {
+ @Override
+ public String getToolTipText(MouseEvent e) {
+ if (table.columnAtPoint(e.getPoint()) == 0) {
+ /*
+ * Tooltip for feature name only
+ */
+ return JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.feature_settings_click_drag"));
+ }
+ return null;
+ }
+ };
table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
table.setFont(new Font("Verdana", Font.PLAIN, 12));
table.setDefaultRenderer(Color.class, new ColorRenderer());
@@ -98,7 +162,27 @@ public class FeatureSettings extends JPanel
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
+ table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
+ evt.getY());
+ }
+ else if (evt.getClickCount() == 2)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(
+ evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
+ evt.isMetaDown(),
+ (String) table.getValueAt(selectedRow, 0));
+ }
+ }
+
+ // isPopupTrigger fires on mouseReleased on Mac
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ selectedRow = table.rowAtPoint(evt.getPoint());
+ if (evt.isPopupTrigger())
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
@@ -131,13 +215,14 @@ public class FeatureSettings extends JPanel
}
}
});
-
+// table.setToolTipText(JvSwingUtils.wrapTooltip(true,
+// MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
dassourceBrowser = new DasSourceBrowser(this);
dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
- if (af.getViewport().featuresDisplayed == null
+ if (af.getViewport().getFeaturesDisplayed() == null
|| fr.renderOrder == null)
{
fr.findAllFeatures(true); // display everything!
@@ -163,25 +248,39 @@ 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);
- dassourceBrowser.fs = null;
- };
- });
+ 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 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()
@@ -194,7 +293,8 @@ 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()
{
@@ -273,8 +373,9 @@ public class FeatureSettings extends JPanel
// probably the color chooser!
table.setValueAt(colorChooser.getColor(), selectedRow, 1);
table.validate();
- me.updateFeatureRenderer(((FeatureTableModel) table
- .getModel()).getData(), false);
+ me.updateFeatureRenderer(
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
}
}
}
@@ -282,6 +383,32 @@ public class FeatureSettings extends JPanel
});
}
}
+ 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, false,
+ 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, false,
+ false, type);
+ }
+ });
+ men.add(selCols);
+ men.add(clearCols);
men.show(table, x, y);
}
@@ -305,15 +432,15 @@ 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;
@@ -398,9 +525,9 @@ public class FeatureSettings extends JPanel
{
public void itemStateChanged(ItemEvent evt)
{
- fr.featureGroups.put(check.getText(), new Boolean(check
- .isSelected()));
- af.alignPanel.seqPanel.seqCanvas.repaint();
+ fr.featureGroups.put(check.getText(),
+ new Boolean(check.isSelected()));
+ af.alignPanel.getSeqPanel().seqCanvas.repaint();
if (af.alignPanel.overviewPanel != null)
{
af.alignPanel.overviewPanel.updateOverviewImage();
@@ -434,10 +561,10 @@ 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)
{
@@ -459,7 +586,9 @@ public class FeatureSettings extends JPanel
|| ((Boolean) fr.featureGroups.get(group)).booleanValue())
{
if (group != null)
+ {
checkGroupState(group);
+ }
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
{
@@ -497,7 +626,9 @@ public class FeatureSettings extends JPanel
if (fr.renderOrder != null)
{
if (!handlingUpdate)
+ {
fr.findAllFeatures(groupChanged != null); // prod to update
+ }
// colourschemes. but don't
// affect display
// First add the checks in the previous render order,
@@ -513,8 +644,8 @@ public class FeatureSettings extends JPanel
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getFeatureStyle(type);
- data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed
- .containsKey(type));
+ data[dataIndex][2] = new Boolean(
+ af.getViewport().getFeaturesDisplayed().containsKey(type));
dataIndex++;
visibleChecks.removeElement(type);
}
@@ -578,23 +709,29 @@ public class FeatureSettings extends JPanel
{
order[i] = fr.getOrder(data[i][0].toString());
if (order[i] < 0)
+ {
order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
+ }
if (i > 1)
+ {
sort = sort || order[i - 1] > order[i];
+ }
}
if (sort)
+ {
jalview.util.QuickSort.sort(order, data);
+ }
}
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.setDialogTitle(MessageManager.getString("label.load_feature_colours"));
+ chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
@@ -608,7 +745,7 @@ public class FeatureSettings extends JPanel
file), "UTF-8");
jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs
+ jucs = jucs
.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
@@ -628,8 +765,8 @@ public class FeatureSettings extends JPanel
Cache.log.warn("Couldn't parse out graduated feature color.",
e);
}
- GraduatedColor gcol = new GraduatedColor(mincol, maxcol, newcol
- .getMin(), newcol.getMax());
+ GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+ newcol.getMin(), newcol.getMax());
if (newcol.hasAutoScale())
{
gcol.setAutoScaled(newcol.getAutoScale());
@@ -652,13 +789,11 @@ public class FeatureSettings extends JPanel
}
if (ttyp.equalsIgnoreCase("ABOVE"))
{
- gcol
- .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
}
if (ttyp.equalsIgnoreCase("BELOW"))
{
- gcol
- .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
}
}
fr.setColour(name = newcol.getName(), gcol);
@@ -688,13 +823,13 @@ 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.setDialogTitle(MessageManager.getString("label.save_feature_colours"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -708,13 +843,13 @@ public class FeatureSettings extends JPanel
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++;
}
@@ -776,7 +911,9 @@ public class FeatureSettings extends JPanel
public void orderByAvWidth()
{
if (table == null || table.getModel() == null)
+ {
return;
+ }
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
float[] width = new float[data.length];
float[] awidth;
@@ -798,7 +935,9 @@ public class FeatureSettings extends JPanel
width[i] = 0;
}
if (max < width[i])
+ {
max = width[i];
+ }
}
boolean sort = false;
for (int i = 0; i < width.length; i++)
@@ -818,11 +957,15 @@ public class FeatureSettings extends JPanel
fr.setOrder(data[i][0].toString(), width[i]); // store for later
}
if (i > 0)
+ {
sort = sort || width[i - 1] > width[i];
+ }
}
if (sort)
+ {
jalview.util.QuickSort.sort(width, data);
// update global priority order
+ }
updateFeatureRenderer(data, false);
table.repaint();
@@ -890,7 +1033,9 @@ public class FeatureSettings extends JPanel
JButton sortByDens = new JButton();
- JPanel transbuttons = new JPanel(new GridLayout(4, 1));
+ JButton help = new JButton();
+
+ JPanel transbuttons = new JPanel(new GridLayout(5, 1));
private void jbInit() throws Exception
{
@@ -898,8 +1043,8 @@ 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)
@@ -907,8 +1052,8 @@ 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)
@@ -916,8 +1061,9 @@ 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)
@@ -925,8 +1071,9 @@ 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)
@@ -934,8 +1081,23 @@ public class FeatureSettings extends JPanel
sortByDens(null);
}
});
- cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- cancel.setText("Cancel");
+ help.setFont(JvSwingUtils.getLabelFont());
+ help.setText(MessageManager.getString("action.help"));
+ help.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.SequenceFeatureSettings);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ cancel.setFont(JvSwingUtils.getLabelFont());
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -944,8 +1106,8 @@ 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)
@@ -953,8 +1115,8 @@ 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)
@@ -962,8 +1124,8 @@ 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)
@@ -975,13 +1137,15 @@ public class FeatureSettings extends JPanel
{
public void stateChanged(ChangeEvent evt)
{
- fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
af.alignPanel.paintAlignment(true);
}
});
transparency.setMaximum(70);
- fetchDAS.setText("Fetch DAS Features");
+ transparency.setToolTipText(MessageManager
+ .getString("label.transparency_tip"));
+ fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
fetchDAS.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -989,7 +1153,7 @@ 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)
@@ -1000,7 +1164,7 @@ 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)
@@ -1009,13 +1173,16 @@ public class FeatureSettings extends JPanel
}
});
this.add(tabbedPane, java.awt.BorderLayout.CENTER);
- tabbedPane.addTab("Feature Settings", settingsPane);
- tabbedPane.addTab("DAS Settings", dasSettingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane);
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
transbuttons.add(optimizeOrder);
transbuttons.add(invert);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
+ transbuttons.add(help);
+ JPanel sliderPanel = new JPanel();
+ sliderPanel.add(transparency);
transPanel.add(transparency);
transPanel.add(transbuttons);
buttonPanel.add(ok);
@@ -1110,7 +1277,7 @@ public class FeatureSettings extends JPanel
System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length);
for (int i = 0; i < typ.length; i++)
{
- if (af.viewport.featuresDisplayed.get(typ[i]) == null)
+ if (af.viewport.getFeaturesDisplayed().get(typ[i]) == null)
{
typ[i] = null;
}
@@ -1123,33 +1290,34 @@ public class FeatureSettings extends JPanel
private String[] getDisplayedFeatureGroups()
{
String[] gps = null;
+ ArrayList _gps = new ArrayList();
if (fr != null)
{
if (fr.featureGroups != null)
{
- Enumeration en = fr.featureGroups.keys();
- gps = new String[fr.featureColours.size()];
+ Iterator en = fr.featureGroups.keySet().iterator();
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())
{
valid = true;
- gps[g++] = gp;
+ _gps.add(gp);
}
}
- while (g < gps.length)
- {
- gps[g++] = null;
- }
if (!valid)
{
return null;
}
+ else
+ {
+ gps = new String[_gps.size()];
+ _gps.toArray(gps);
+ }
}
}
return gps;
@@ -1171,7 +1339,7 @@ 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;
@@ -1219,9 +1387,9 @@ public class FeatureSettings extends JPanel
* 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);
}
/**
@@ -1247,14 +1415,15 @@ public class FeatureSettings extends JPanel
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;
+ final List dassources = resolved;
fetchDAS.setEnabled(false);
// cancelDAS.setEnabled(true); doDasFetch does this.
Runnable fetcher = new Runnable()
@@ -1288,7 +1457,7 @@ public class FeatureSettings extends JPanel
fetchDAS.setEnabled(true);
cancelDAS.setEnabled(false);
dassourceBrowser.setGuiEnabled(true);
-
+
}
public void cancelDAS_actionPerformed(ActionEvent e)
@@ -1303,11 +1472,15 @@ public class FeatureSettings extends JPanel
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,
- JOptionPane.INFORMATION_MESSAGE);
+ JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.no_das_sources_selected_warn"),
+ MessageManager
+ .getString("label.no_das_sources_selected_title"),
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.INFORMATION_MESSAGE);
}
// ///////////////////////////////////////////////////////////////////////
@@ -1321,7 +1494,7 @@ public class FeatureSettings extends JPanel
}
private String[] columnNames =
- { "Feature Type", "Colour", "Display" };
+ { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") };
private Object[][] data;
@@ -1586,7 +1759,7 @@ class FeatureIcon implements Icon
// width/g.getFontMetrics().stringWidth("Label"),
// height/g.getFontMetrics().getHeight())));
- g.drawString("Label", 0, 0);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
}
else