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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
src
/
jalview
/
appletgui
/
FeatureSettings.java
diff --git
a/src/jalview/appletgui/FeatureSettings.java
b/src/jalview/appletgui/FeatureSettings.java
index
b51906d
..
01e096e
100755
(executable)
--- a/
src/jalview/appletgui/FeatureSettings.java
+++ b/
src/jalview/appletgui/FeatureSettings.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-64,7
+64,7
@@
import java.util.Vector;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener
+ AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
{
FeatureRenderer fr;
@@
-114,12
+114,13
@@
public class FeatureSettings extends Panel implements ItemListener,
fr.findAllFeatures(true); // was default - now true to make all visible
}
fr.findAllFeatures(true); // was default - now true to make all visible
}
- setTableData();
+ discoverAllFeatureData();
this.setLayout(new BorderLayout());
scrollPane = new ScrollPane();
scrollPane.add(featurePanel);
this.setLayout(new BorderLayout());
scrollPane = new ScrollPane();
scrollPane.add(featurePanel);
- if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
{
add(scrollPane, BorderLayout.CENTER);
}
{
add(scrollPane, BorderLayout.CENTER);
}
@@
-150,10
+151,11
@@
public class FeatureSettings extends Panel implements ItemListener,
if (groupPanel != null)
{
if (groupPanel != null)
{
- groupPanel
- .setLayout(new GridLayout(
- (fr.getFeatureGroupsSize()) / 4 + 1,
- 4)); // JBPNote - this was scaled on number of visible groups. seems broken
+ 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);
groupPanel.validate();
add(groupPanel, BorderLayout.NORTH);
@@
-179,8
+181,8
@@
public class FeatureSettings extends Panel implements ItemListener,
height = Math.min(400, height);
int width = 300;
jalview.bin.JalviewLite.addFrame(frame,
height = Math.min(400, height);
int width = 300;
jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.getString("label.feature_settings"), width,
- height);
+ MessageManager.getString("label.sequence_feature_settings"),
+ width, height);
}
public void paint(Graphics g)
}
public void paint(Graphics g)
@@
-202,8
+204,7
@@
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(
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 }));
+ "label.settings_for_type", new String[] { type }));
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
@@
-213,8
+214,8
@@
public class FeatureSettings extends Panel implements ItemListener,
public void actionPerformed(ActionEvent e)
{
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
- { type });
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureScore(new String[] { type });
}
});
}
});
@@
-225,8
+226,8
@@
public class FeatureSettings extends Panel implements ItemListener,
public void actionPerformed(ActionEvent e)
{
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
- { type });
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureDensity(new String[] { type });
}
});
}
});
@@
-279,9
+280,11
@@
public class FeatureSettings extends Panel implements ItemListener,
men.show(this.featurePanel, x, y);
}
men.show(this.featurePanel, x, y);
}
- public void setTableData()
+ @Override
+ public void discoverAllFeatureData()
{
{
- if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
{
rebuildGroups();
{
rebuildGroups();
@@
-306,7
+309,7
@@
public class FeatureSettings extends Panel implements ItemListener,
}
// TODO: JAL-964 - smoothly incorporate new group entries if panel already
// displayed and new groups present
}
// TODO: JAL-964 - smoothly incorporate new group entries if panel already
// displayed and new groups present
- for (String group:fr.getFeatureGroups())
+ for (String group : fr.getFeatureGroups())
{
boolean vis = fr.checkGroupVisibility(group, false);
Checkbox check = new MyCheckbox(group, vis,
{
boolean vis = fr.checkGroupVisibility(group, false);
Checkbox check = new MyCheckbox(group, vis,
@@
-324,6
+327,7
@@
public class FeatureSettings extends Panel implements ItemListener,
groupPanel.validate();
}
}
groupPanel.validate();
}
}
+
// This routine adds and removes checkboxes depending on
// Group selection states
void resetTable(boolean groupsChanged)
// This routine adds and removes checkboxes depending on
// Group selection states
void resetTable(boolean groupsChanged)
@@
-480,11
+484,12
@@
public class FeatureSettings extends Panel implements ItemListener,
selectionChanged();
}
selectionChanged();
}
- private ItemListener groupItemListener = new ItemListener() {
- public void itemStateChanged(ItemEvent evt) {
+ private ItemListener groupItemListener = new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
Checkbox source = (Checkbox) evt.getSource();
Checkbox source = (Checkbox) evt.getSource();
- fr.setGroupVisibility(source.getLabel(),
- source.getState());
+ fr.setGroupVisibility(source.getLabel(), source.getState());
ap.seqPanel.seqCanvas.repaint();
if (ap.overviewPanel != null)
{
ap.seqPanel.seqCanvas.repaint();
if (ap.overviewPanel != null)
{
@@
-494,6
+499,7
@@
public class FeatureSettings extends Panel implements ItemListener,
return;
};
};
return;
};
};
+
public void itemStateChanged(ItemEvent evt)
{
selectionChanged();
public void itemStateChanged(ItemEvent evt)
{
selectionChanged();
@@
-613,7
+619,9
@@
public class FeatureSettings extends Panel implements ItemListener,
}
else
{
}
else
{
- throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_unsupported_feature_colour_object"));
}
refreshTable();
}
}
refreshTable();
}
@@
-709,7
+717,9
@@
public class FeatureSettings extends Panel implements ItemListener,
}
else
{
}
else
{
- throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_colour_for_mycheckbox"));
}
if (col != null)
{
}
if (col != null)
{