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Merge branch 'develop' into features/JAL-1648_cache_user_inputs
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationColumnChooser.java
diff --git
a/src/jalview/gui/AnnotationColumnChooser.java
b/src/jalview/gui/AnnotationColumnChooser.java
index
00ccbf0
..
a15f605
100644
(file)
--- a/
src/jalview/gui/AnnotationColumnChooser.java
+++ b/
src/jalview/gui/AnnotationColumnChooser.java
@@
-21,8
+21,7
@@
package jalview.gui;
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.io.cache.JvCacheableInputBox;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
import jalview.io.cache.JvCacheableInputBox;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
@@
-31,6
+30,7
@@
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
@@
-85,7
+85,11
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
private int actionOption = ACTION_OPTION_SELECT;
private int actionOption = ACTION_OPTION_SELECT;
- private ColumnSelection oldColumnSelection;
+ private HiddenColumns oldHiddenColumns;
+
+ protected int MIN_WIDTH = 420;
+
+ protected int MIN_HEIGHT = 430;
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
@@
-96,6
+100,7
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
Desktop.addInternalFrame(frame,
MessageManager.getString("label.select_by_annotation"), 520,
215);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.select_by_annotation"), 520,
215);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
addSliderChangeListener();
addSliderMouseListeners();
@@
-104,25
+109,28
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
{
return;
}
{
return;
}
- setOldColumnSelection(av.getColumnSelection());
+ setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
adjusting = true;
setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
-
+ AnnotationColumnChooser lastChooser = av
+ .getAnnotationColumnSelectionState();
// restore Object state from the previous session if one exists
// restore Object state from the previous session if one exists
- if (av.getAnnotationColumnSelectionState() != null)
+ if (lastChooser != null)
{
{
- currentSearchPanel = av.getAnnotationColumnSelectionState()
+ currentSearchPanel = lastChooser
.getCurrentSearchPanel();
.getCurrentSearchPanel();
- currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+ currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
.getCurrentStructureFilterPanel();
- annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ annotations.setSelectedIndex(lastChooser
.getAnnotations().getSelectedIndex());
.getAnnotations().getSelectedIndex());
- threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ threshold.setSelectedIndex(lastChooser
.getThreshold().getSelectedIndex());
.getThreshold().getSelectedIndex());
- actionOption = av.getAnnotationColumnSelectionState()
+ actionOption = lastChooser
.getActionOption();
.getActionOption();
+ percentThreshold.setSelected(lastChooser.percentThreshold
+ .isSelected());
}
try
}
try
@@
-150,6
+158,9
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ percentThreshold.setBackground(Color.white);
+ percentThreshold.setFont(JvSwingUtils.getLabelFont());
+
JPanel actionPanel = new JPanel();
actionPanel.setBackground(Color.white);
actionPanel.setFont(JvSwingUtils.getLabelFont());
JPanel actionPanel = new JPanel();
actionPanel.setBackground(Color.white);
actionPanel.setFont(JvSwingUtils.getLabelFont());
@@
-173,8
+184,9
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.add(getThreshold());
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.add(getThreshold());
- thresholdPanel.add(thresholdValue, "wrap");
- thresholdPanel.add(slider, "grow, span, wrap");
+ thresholdPanel.add(percentThreshold, "wrap");
+ thresholdPanel.add(slider, "grow");
+ thresholdPanel.add(thresholdValue, "span, wrap");
actionPanel.add(ok);
actionPanel.add(cancel);
actionPanel.add(ok);
actionPanel.add(cancel);
@@
-223,26
+235,26
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
@Override
protected void reset()
{
@Override
protected void reset()
{
- if (this.getOldColumnSelection() != null)
+ if (this.getOldHiddenColumns() != null)
{
av.getColumnSelection().clear();
if (av.getAnnotationColumnSelectionState() != null)
{
{
av.getColumnSelection().clear();
if (av.getAnnotationColumnSelectionState() != null)
{
- ColumnSelection oldSelection = av
+ HiddenColumns oldHidden = av
.getAnnotationColumnSelectionState()
.getAnnotationColumnSelectionState()
- .getOldColumnSelection();
- if (oldSelection != null && oldSelection.getHiddenColumns() != null
- && !oldSelection.getHiddenColumns().isEmpty())
+ .getOldHiddenColumns();
+ if (oldHidden != null && oldHidden.getHiddenRegions() != null
+ && !oldHidden.getHiddenRegions().isEmpty())
{
{
- for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
+ for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
.iterator(); itr.hasNext();)
{
int positions[] = itr.next();
av.hideColumns(positions[0], positions[1]);
}
}
.iterator(); itr.hasNext();)
{
int positions[] = itr.next();
av.hideColumns(positions[0], positions[1]);
}
}
- av.setColumnSelection(oldSelection);
+ av.getAlignment().setHiddenColumns(oldHidden);
}
ap.paintAlignment(true);
}
}
ap.paintAlignment(true);
}
@@
-281,12
+293,14
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
slider.setEnabled(true);
thresholdValue.setEnabled(true);
slider.setEnabled(true);
thresholdValue.setEnabled(true);
+ percentThreshold.setEnabled(true);
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
+ percentThreshold.setEnabled(false);
// build filter params
}
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
// build filter params
}
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
@@
-307,7
+321,9
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+
+ setThresholdValueText();
+
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
@@
-316,7
+332,7
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
// build filter params
filterParams
.setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
// build filter params
filterParams
.setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
- if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+ if (getCurrentAnnotation().isQuantitative())
{
filterParams
.setThresholdValue(getCurrentAnnotation().threshold.value);
{
filterParams
.setThresholdValue(getCurrentAnnotation().threshold.value);
@@
-384,16
+400,16
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
ap.paintAlignment(true);
}
ap.paintAlignment(true);
}
- public ColumnSelection getOldColumnSelection()
+ public HiddenColumns getOldHiddenColumns()
{
{
- return oldColumnSelection;
+ return oldHiddenColumns;
}
}
- public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+ public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
{
{
- if (currentColumnSelection != null)
+ if (currentHiddenColumns != null)
{
{
- this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+ this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
}
}
}
}
@@
-469,8
+485,9
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
- if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+ if (av.getAlignment()
+ .getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]].isQuantitative())
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}