+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.appletgui;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.gui.JvSwingUtils;
+import jalview.datamodel.HiddenColumns;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import java.util.Iterator;
import java.util.Vector;
-import net.miginfocom.swing.MigLayout;
+//import javax.swing.JPanel;
+
+//import net.miginfocom.swing.MigLayout;
public class AnnotationColumnChooser extends AnnotationRowFilter implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
private BorderLayout borderLayout1 = new BorderLayout();
+ private BorderLayout gBorderLayout = new BorderLayout();
+
+ private BorderLayout ngBorderLayout = new BorderLayout();
+
private Choice threshold = new Choice();
private StructureFilterPanel gStructureFilterPanel;
private int actionOption = ACTION_OPTION_SELECT;
- private ColumnSelection oldColumnSelection;
+ private HiddenColumns oldHiddenColumns;
public AnnotationColumnChooser()
{
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- if (av.getAlignment().getAlignmentAnnotation() == null)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
{
return;
}
- setOldColumnSelection(av.getColumnSelection());
+ setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
- Vector list = new Vector();
+ Vector<String> list = new Vector<String>();
int index = 1;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < anns.length; i++)
{
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ String label = anns[i].label;
+ if (anns[i].sequenceRef != null)
+ {
+ label = label + "_" + anns[i].sequenceRef.getName();
+ }
if (!list.contains(label))
{
list.addElement(label);
slider.setPreferredSize(new Dimension(100, 32));
thresholdPanel.setBackground(Color.white);
- thresholdPanel.setFont(JvSwingUtils.getLabelFont());
- thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
+ // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
actionPanel.setBackground(Color.white);
- actionPanel.setFont(JvSwingUtils.getLabelFont());
+ // actionPanel.setFont(JvSwingUtils.getLabelFont());
- graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ graphFilterView.setLayout(gBorderLayout);
graphFilterView.setBackground(Color.white);
- noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ noGraphFilterView.setLayout(ngBorderLayout);
noGraphFilterView.setBackground(Color.white);
annotationComboBoxPanel.setBackground(Color.white);
- annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
+ // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
gSearchPanel = new SearchPanel(this);
ngSearchPanel = new SearchPanel(this);
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.setTitle("Threshold Filter");
- thresholdPanel.add(getThreshold(), "grow");
- thresholdPanel.add(thresholdValue, "grow, wrap");
- thresholdPanel.add(slider, "grow, span, wrap");
+ thresholdPanel.add(getThreshold());
+ thresholdPanel.add(slider);
+ thresholdPanel.add(thresholdValue);
actionPanel.add(ok);
actionPanel.add(cancel);
- graphFilterView.add(gSearchPanel, "grow, span, wrap");
- graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
- graphFilterView.add(thresholdPanel, "grow, span, wrap");
- graphFilterView.add(gFurtherActionPanel);
+ Panel staticPanel = new Panel();
+ staticPanel.setLayout(new BorderLayout());
+ staticPanel.setBackground(Color.white);
+
+ staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
+ staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
+
+ graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
+ graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
+ graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
- noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
- noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
- noGraphFilterView.add(ngFurtherActionPanel);
+ noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
+ noGraphFilterView.add(ngStructureFilterPanel,
+ java.awt.BorderLayout.CENTER);
+ noGraphFilterView.add(ngFurtherActionPanel,
+ java.awt.BorderLayout.CENTER);
annotationComboBoxPanel.add(getAnnotations());
switchableViewsPanel.add(noGraphFilterView,
this.validate();
}
+ @Override
@SuppressWarnings("unchecked")
public void reset()
{
- if (this.getOldColumnSelection() != null)
+ if (this.getOldHiddenColumns() != null)
{
av.getColumnSelection().clear();
if (av.getAnnotationColumnSelectionState() != null)
{
- ColumnSelection oldSelection = av
+ HiddenColumns oldHidden = av
.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]);
}
}
- av.setColumnSelection(oldSelection);
+ av.getAlignment().setHiddenColumns(oldHidden);
}
ap.paintAlignment(true);
}
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
});
}
+ @Override
public void valueChanged(boolean updateAllAnnotation)
{
if (slider.isEnabled())
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);
}
}
updateView();
}
- public class FurtherActionPanel extends Panel implements
- ItemListener
+ public class FurtherActionPanel extends Panel implements ItemListener
{
private AnnotationColumnChooser aColChooser;
this.setBackground(Color.white);
this.setTitle("Structure Filter");
- this.setFont(JvSwingUtils.getLabelFont());
+ // this.setFont(JvSwingUtils.getLabelFont());
this.add(all);
this.add(alphaHelix);
});
- displayName.setLabel(MessageManager.getString("label.display_name"));
+ displayName.setLabel(MessageManager.getString("label.label"));
displayName.setEnabled(false);
displayName.addItemListener(this);
description.setEnabled(false);
description.addItemListener(this);
this.setTitle("Search Filter");
- this.setFont(JvSwingUtils.getLabelFont());
+ // this.setFont(JvSwingUtils.getLabelFont());
syncState();
this.add(searchBox);
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)