X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=584a69a52c46ece5053ac47db499157610eab73b;hb=d82ec00f14199ef0ce21bd5bc70a59142b7c4b07;hp=378289ab905ee74ae710ee09ede150d3efead03c;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 378289a..584a69a 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,38 +1,71 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * 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.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.commands.OrderCommand;
-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.Arrays;
+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;
@@ -48,8 +81,6 @@ public class FeatureSettings extends Panel implements ItemListener,
ScrollPane scrollPane;
- boolean alignmentHasFeatures = false;
-
Image linkImage;
Scrollbar transparency;
@@ -62,9 +93,9 @@ 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);
}
@@ -79,17 +110,18 @@ 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);
}
@@ -102,7 +134,7 @@ 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);
@@ -120,10 +152,11 @@ public class FeatureSettings extends Panel implements ItemListener,
if (groupPanel != null)
{
- groupPanel
- .setLayout(new GridLayout(
- (fr.featureGroups.size() - fr.hiddenGroups.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);
@@ -133,6 +166,7 @@ public class FeatureSettings extends Panel implements ItemListener,
final FeatureSettings me = this;
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
if (me.av.featureSettings == me)
@@ -148,16 +182,23 @@ 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, MessageManager.getString("label.feature_settings"), width,
- height);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ width, height);
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.black);
- g.drawString(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);
+ g.drawString(MessageManager
+ .getString("label.no_features_added_to_this_alignment"), 10, 20);
+ g.drawString(MessageManager
+ .getString("label.features_can_be_added_from_searches_1"), 10,
+ 40);
+ g.drawString(MessageManager
+ .getString("label.features_can_be_added_from_searches_2"), 10,
+ 60);
}
protected void popupSort(final MyCheckbox check, final Hashtable minmax,
@@ -165,28 +206,33 @@ public class FeatureSettings extends Panel implements ItemListener,
{
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"));
+ 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.sortByScore(new String[]
- { type });
+ me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
+ .asList(new String[] { type }));
}
});
- MenuItem dens = new MenuItem(MessageManager.getString("label.sort_by_density"));
+ MenuItem dens = new MenuItem(
+ MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.sortByDens(new String[]
- { type });
+ me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
+ .asList(new String[] { type }));
}
});
@@ -217,6 +263,7 @@ public class FeatureSettings extends Panel implements ItemListener,
mxcol.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
if (typeCol instanceof Color)
@@ -239,10 +286,11 @@ public class FeatureSettings extends Panel implements ItemListener,
men.show(this.featurePanel, x, y);
}
- public void setTableData()
+ @Override
+ public void discoverAllFeatureData()
{
- alignmentHasFeatures = fr.buildGroupHash();
- if (alignmentHasFeatures)
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
{
rebuildGroups();
@@ -267,18 +315,15 @@ public class FeatureSettings extends Panel implements ItemListener,
}
// TODO: JAL-964 - smoothly incorporate new group entries if panel already
// displayed and new groups present
- 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)));
+ for (String group : fr.getFeatureGroups())
+ {
+ boolean vis = fr.checkGroupVisibility(group, false);
+ Checkbox check = new MyCheckbox(group, vis, false);
check.addMouseListener(this);
check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(this);
- check.setVisible(fr.hiddenGroups.contains(group));
+ check.addItemListener(groupItemListener);
+ // note - visibility seems to correlate with displayed. ???wtf ??
+ check.setVisible(vis);
groupPanel.add(check);
}
if (rdrw)
@@ -308,8 +353,7 @@ public class FeatureSettings extends Panel implements ItemListener,
{
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))
@@ -338,13 +382,14 @@ 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))
{
@@ -406,15 +451,12 @@ 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;
}
- check = new MyCheckbox(
- type,
- selected,
- (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+ check = new MyCheckbox(type, selected, false,
fr.getFeatureStyle(type));
check.addMouseListener(this);
@@ -433,6 +475,7 @@ public class FeatureSettings extends Panel implements ItemListener,
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
for (int i = 0; i < featurePanel.getComponentCount(); i++)
@@ -443,26 +486,26 @@ public class FeatureSettings extends Panel implements ItemListener,
selectionChanged();
}
- public void itemStateChanged(ItemEvent evt)
+ private ItemListener groupItemListener = new ItemListener()
{
- if (evt != null)
+ @Override
+ public void itemStateChanged(ItemEvent evt)
{
- // Is the source a top level featureGroup?
Checkbox source = (Checkbox) evt.getSource();
- if (fr.featureGroups.containsKey(source.getLabel()))
+ fr.setGroupVisibility(source.getLabel(), source.getState());
+ ap.seqPanel.seqCanvas.repaint();
+ if (ap.overviewPanel != null)
{
- fr.featureGroups.put(source.getLabel(),
- new Boolean(source.getState()));
- ap.seqPanel.seqCanvas.repaint();
- if (ap.overviewPanel != null)
- {
- ap.overviewPanel.updateOverviewImage();
- }
-
- resetTable(true);
- return;
+ ap.overviewPanel.updateOverviewImage();
}
- }
+ resetTable(true);
+ return;
+ };
+ };
+
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
selectionChanged();
}
@@ -494,22 +537,7 @@ public class FeatureSettings extends Panel implements ItemListener,
boolean dragging = false;
- public void mousePressed(MouseEvent evt)
- {
-
- selectedCheck = (MyCheckbox) evt.getSource();
-
- if (fr.featureLinks != null
- && fr.featureLinks.containsKey(selectedCheck.type))
- {
- if (evt.getX() > selectedCheck.stringWidth + 20)
- {
- evt.consume();
- }
- }
-
- }
-
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (((Component) evt.getSource()).getParent() != featurePanel)
@@ -519,6 +547,7 @@ public class FeatureSettings extends Panel implements ItemListener,
dragging = true;
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (((Component) evt.getSource()).getParent() != featurePanel)
@@ -581,7 +610,8 @@ public class FeatureSettings extends Panel implements ItemListener,
else
{
throw new Error(
- "Implementation error: Unsupported feature colour object.");
+ MessageManager
+ .getString("error.implementation_error_unsupported_feature_colour_object"));
}
refreshTable();
}
@@ -593,30 +623,23 @@ public class FeatureSettings extends Panel implements ItemListener,
ap.paintAlignment(true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
MyCheckbox check = (MyCheckbox) evt.getSource();
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
{
- this.popupSort(check, fr.minmax, evt.getX(), evt.getY());
- }
- if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
- {
- if (evt.getX() > check.stringWidth + 20)
- {
- evt.consume();
- String link = fr.featureLinks.get(check.type).toString();
- ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
- link.substring(0, link.indexOf("|")));
- }
+ this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
}
if (check.getParent() != featurePanel)
@@ -640,13 +663,15 @@ public class FeatureSettings extends Panel implements ItemListener,
}
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- fr.transparency = ((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
ap.seqPanel.seqCanvas.repaint();
}
@@ -677,7 +702,9 @@ public class FeatureSettings extends Panel implements ItemListener,
}
else
{
- throw new Error("Invalid color for MyCheckBox");
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_colour_for_mycheckbox"));
}
if (col != null)
{
@@ -722,6 +749,7 @@ public class FeatureSettings extends Panel implements ItemListener,
updateColor(featureStyle);
}
+ @Override
public void paint(Graphics g)
{
Dimension d = getSize();
@@ -760,81 +788,9 @@ public class FeatureSettings extends Panel implements ItemListener,
}
}
- 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)
+ @Override
+ public void mousePressed(MouseEvent e)
{
- sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
}
}