X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=1dce93648449902d1474c6cc77aa3e2186131cc5;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=9b2dba671aecb94262ad65ed6367d3937f500f53;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 9b2dba6..1dce936 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,36 +1,70 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.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;
@@ -46,8 +80,6 @@ public class FeatureSettings extends Panel implements ItemListener,
ScrollPane scrollPane;
- boolean alignmentHasFeatures = false;
-
Image linkImage;
Scrollbar transparency;
@@ -60,9 +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);
}
@@ -77,17 +109,18 @@ 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);
}
@@ -100,7 +133,7 @@ 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);
@@ -118,8 +151,11 @@ 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);
@@ -144,16 +180,22 @@ 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,
- height);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.sequence_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);
}
protected void popupSort(final MyCheckbox check, final Hashtable minmax,
@@ -161,8 +203,10 @@ public class FeatureSettings extends Panel implements ItemListener,
{
final String type = check.type;
final Object typeCol = fr.getFeatureStyle(type);
- java.awt.PopupMenu men = new PopupMenu("Settings for " + type);
- java.awt.MenuItem scr = new MenuItem("Sort by Score");
+ 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()
@@ -170,19 +214,20 @@ public class FeatureSettings extends Panel implements ItemListener,
public void actionPerformed(ActionEvent e)
{
- me.sortByScore(new String[]
- { type });
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureScore(new String[] { type });
}
});
- MenuItem dens = new MenuItem("Sort by Density");
+ MenuItem dens = new MenuItem(
+ MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- me.sortByDens(new String[]
- { type });
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureDensity(new String[] { type });
}
});
@@ -235,10 +280,11 @@ 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();
@@ -261,18 +307,19 @@ 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)
@@ -288,22 +335,21 @@ 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))
@@ -332,13 +378,14 @@ 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))
{
@@ -400,7 +447,7 @@ 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;
}
@@ -437,26 +484,24 @@ public class FeatureSettings extends Panel implements ItemListener,
selectionChanged();
}
- public void itemStateChanged(ItemEvent evt)
+ private ItemListener groupItemListener = new ItemListener()
{
- if (evt != null)
+ 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;
+ };
+ };
+
+ public void itemStateChanged(ItemEvent evt)
+ {
selectionChanged();
}
@@ -575,7 +620,8 @@ 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();
}
@@ -600,7 +646,7 @@ public class FeatureSettings extends Panel implements ItemListener,
MyCheckbox check = (MyCheckbox) evt.getSource();
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
{
- this.popupSort(check, fr.minmax, evt.getX(), evt.getY());
+ this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
}
if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
{
@@ -640,7 +686,7 @@ 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();
}
@@ -671,7 +717,9 @@ 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)
{
@@ -754,81 +802,4 @@ 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)
- {
- sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
- }
-
}