X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=2b79256dd621e607d4c19534df4bf7a63aa65d3c;hb=06e3a52df5af8243cdb67c023c8ddd834711ad36;hp=4649786f1c363ff5c37f6b6736824885ac20a662;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 4649786..2b79256 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,33 +1,70 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+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.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener
+ AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
@@ -43,8 +80,6 @@ public class FeatureSettings extends Panel implements ItemListener,
ScrollPane scrollPane;
- boolean alignmentHasFeatures = false;
-
Image linkImage;
Scrollbar transparency;
@@ -57,9 +92,9 @@ public class FeatureSettings extends Panel implements ItemListener,
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)
+ if (fr.isTransparencyAvailable())
{
transparency.addAdjustmentListener(this);
}
@@ -74,17 +109,17 @@ public class FeatureSettings extends Panel implements ItemListener,
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);
}
@@ -97,7 +132,7 @@ public class FeatureSettings extends Panel implements ItemListener,
Panel tPanel = new Panel(new BorderLayout());
- if (fr.transparencySetter != null)
+ if (fr.isTransparencyAvailable())
{
tPanel.add(transparency, BorderLayout.CENTER);
tPanel.add(new Label("Transparency"), BorderLayout.EAST);
@@ -115,8 +150,10 @@ public class FeatureSettings extends Panel implements ItemListener,
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);
@@ -141,22 +178,111 @@ public class FeatureSettings extends Panel implements ItemListener,
height = Math.max(200, height);
height = Math.min(400, height);
int width = 300;
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.feature_settings"), width,
height);
}
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);
}
- public void setTableData()
+ protected void popupSort(final MyCheckbox check, final Hashtable minmax,
+ int x, int y)
{
- alignmentHasFeatures = fr.buildGroupHash();
- if (alignmentHasFeatures)
+ final String type = check.type;
+ final Object typeCol = fr.getFeatureStyle(type);
+ java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
+ "label.settings_for_type", new String[]
+ { type }));
+ java.awt.MenuItem scr = new MenuItem(
+ MessageManager.getString("label.sort_by_score"));
+ men.add(scr);
+ final FeatureSettings me = this;
+ scr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
+ { type });
+ }
+
+ });
+ MenuItem dens = new MenuItem(
+ MessageManager.getString("label.sort_by_density"));
+ dens.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(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);
+ }
+
+ @Override
+ public void discoverAllFeatureData()
+ {
+ if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
{
rebuildGroups();
@@ -179,18 +305,19 @@ public class FeatureSettings extends Panel implements ItemListener,
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(),
+ boolean vis = fr.checkGroupVisibility(group, false);
+ Checkbox check = new MyCheckbox(group, vis,
(fr.featureLinks != null && fr.featureLinks
.containsKey(group)));
check.addMouseListener(this);
check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(this);
+ check.addItemListener(groupItemListener);
+ // note - visibility seems to correlate with displayed. ???wtf ??
+ check.setVisible(vis);
groupPanel.add(check);
}
if (rdrw)
@@ -198,7 +325,6 @@ public class FeatureSettings extends Panel implements ItemListener,
groupPanel.validate();
}
}
-
// This routine adds and removes checkboxes depending on
// Group selection states
void resetTable(boolean groupsChanged)
@@ -206,22 +332,21 @@ public class FeatureSettings extends Panel implements ItemListener,
SequenceFeature[] tmpfeatures;
String group = null, type;
Vector visibleChecks = new Vector();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ 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))
@@ -235,14 +360,14 @@ public class FeatureSettings extends Panel implements ItemListener,
Component[] comps;
int cSize = featurePanel.getComponentCount();
- Checkbox check;
+ 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--;
@@ -250,13 +375,14 @@ public class FeatureSettings extends Panel implements ItemListener,
}
}
- 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 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))
{
@@ -294,21 +420,21 @@ public class FeatureSettings extends Panel implements ItemListener,
* 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
+ * 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.
+ * 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;
@@ -318,7 +444,7 @@ public class FeatureSettings extends Panel implements ItemListener,
if (addCheck)
{
boolean selected = false;
- if (groupsChanged || av.featuresDisplayed.containsKey(type))
+ if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
{
selected = true;
}
@@ -326,11 +452,11 @@ public class FeatureSettings extends Panel implements ItemListener,
check = new MyCheckbox(
type,
selected,
- (fr.featureLinks != null && fr.featureLinks.containsKey(type)));
+ (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+ fr.getFeatureStyle(type));
check.addMouseListener(this);
check.addMouseMotionListener(this);
- check.setBackground(fr.getColour(type));
check.addItemListener(this);
if (groupsChanged)
{
@@ -355,26 +481,22 @@ public class FeatureSettings extends Panel implements ItemListener,
selectionChanged();
}
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt != null)
- {
- // Is the source a top level featureGroup?
+ private ItemListener groupItemListener = new ItemListener() {
+ public void itemStateChanged(ItemEvent evt) {
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;
+ };
+ };
+ public void itemStateChanged(ItemEvent evt)
+ {
selectionChanged();
}
@@ -387,9 +509,9 @@ public class FeatureSettings extends Panel implements ItemListener,
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++;
}
@@ -412,7 +534,7 @@ public class FeatureSettings extends Panel implements ItemListener,
selectedCheck = (MyCheckbox) evt.getSource();
if (fr.featureLinks != null
- && fr.featureLinks.containsKey(selectedCheck.getLabel()))
+ && fr.featureLinks.containsKey(selectedCheck.type))
{
if (evt.getX() > selectedCheck.stringWidth + 20)
{
@@ -483,9 +605,22 @@ public class FeatureSettings extends Panel implements ItemListener,
}
}
- 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(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
+ }
+ refreshTable();
+ }
+
+ public void refreshTable()
{
- fr.setColour(feature, col);
featurePanel.removeAll();
resetTable(false);
ap.paintAlignment(true);
@@ -502,16 +637,18 @@ public class FeatureSettings extends Panel implements ItemListener,
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.getMinMax(), evt.getX(), evt.getY());
+ }
+ if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
{
if (evt.getX() > check.stringWidth + 20)
{
evt.consume();
- String link = fr.featureLinks.get(check.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("|")));
}
}
@@ -522,8 +659,17 @@ public class FeatureSettings extends Panel implements ItemListener,
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));
+ }
}
}
@@ -533,28 +679,112 @@ public class FeatureSettings extends Panel implements ItemListener,
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- fr.transparency = ((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
ap.seqPanel.seqCanvas.repaint();
}
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(MessageManager.getString("error.invalid_colour_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,
@@ -562,4 +792,5 @@ public class FeatureSettings extends Panel implements ItemListener,
}
}
}
+
}