-/*
- * 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.api.FeatureSettingsControllerI;
-import jalview.bin.JalviewLite;
-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 javax.swing.JButton;
-import javax.swing.JCheckBox;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import javax.swing.JFrame;
-import java.awt.Graphics;
-import java.awt.GridLayout;
-import java.awt.Image;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JScrollPane;
-import javax.swing.JScrollBar;
-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 JPanel implements ItemListener,
- MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener, FeatureSettingsControllerI
-{
- FeatureRenderer fr;
-
- AlignmentPanel ap;
-
- AlignViewport av;
-
- JFrame frame;
-
- JPanel groupPanel;
-
- JPanel featurePanel = new JPanel();
-
- JScrollPane scrollPane;
-
- Image linkImage;
-
- JScrollBar transparency;
-
- public FeatureSettings(final AlignmentPanel ap)
- {
- this.ap = ap;
- this.av = ap.av;
- ap.av.featureSettings = this;
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
-
- transparency = new JScrollBar(JScrollBar.HORIZONTAL,
- 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
-
- if (fr.isTransparencyAvailable())
- {
- transparency.addAdjustmentListener(this);
- }
- else
- {
- transparency.setEnabled(false);
- }
-
- java.net.URL url = getClass().getResource("/images/link.gif");
- if (url != null)
- {
- linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
- }
-
- if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())
- {
- fr.findAllFeatures(true); // was default - now true to make all visible
- }
-
- discoverAllFeatureData();
-
- this.setLayout(new BorderLayout());
- scrollPane = new JScrollPane();
- scrollPane.add(featurePanel);
- if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
- {
- add(scrollPane, BorderLayout.CENTER);
- }
-
- JButton invert = new JButton("Invert Selection");
- invert.addActionListener(this);
-
- JPanel lowerPanel = new JPanel(new GridLayout(2, 1, 5, 10));
- lowerPanel.add(invert);
-
- JPanel tPanel = new JPanel(new BorderLayout());
-
- if (fr.isTransparencyAvailable())
- {
- tPanel.add(transparency, BorderLayout.CENTER);
- tPanel.add(new JLabel("Transparency"), BorderLayout.EAST);
- }
- else
- {
- tPanel.add(
- new JLabel("Transparency not available in this web browser"),
- BorderLayout.CENTER);
- }
-
- lowerPanel.add(tPanel, BorderLayout.SOUTH);
-
- add(lowerPanel, BorderLayout.SOUTH);
-
- if (groupPanel != null)
- {
- 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);
- }
- frame = new JFrame();
- frame.add(this);
- final FeatureSettings me = this;
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- if (me.av.featureSettings == me)
- {
- me.av.featureSettings = null;
- me.ap = null;
- me.av = null;
- }
- }
- });
- int height = featurePanel.getComponentCount() * 50 + 60;
-
- height = Math.max(200, height);
- height = Math.min(400, height);
- int width = 300;
- JalviewLite.addFrame(frame,
- MessageManager.getString("label.feature_settings"), width,
- height);
- }
-
- 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);
- }
-
- protected void popupSort(final MyCheckbox check, final Hashtable minmax,
- int x, int y)
- {
- final String type = check.type;
- final Object typeCol = fr.getFeatureStyle(type);
- JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
- "label.settings_for_type", new String[]
- { type }));
- JMenuItem scr = new JMenuItem(
- MessageManager.getString("label.sort_by_score"));
- men.add(scr);
- final FeatureSettings me = this;
- scr.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
- { type });
- }
-
- });
- JMenuItem dens = new JMenuItem(
- MessageManager.getString("label.sort_by_density"));
- dens.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
- { type });
- }
-
- });
- men.add(dens);
- if (minmax != null)
- {
- final Object typeMinMax = minmax.get(type);
- /*
- * final java.awt.CheckboxMenuItem chb = new
- * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
- * moment chb.setState(minmax.get(type) != null);
- * chb.addActionListener(new ActionListener() {
- *
- * public void actionPerformed(ActionEvent e) {
- * chb.setState(chb.isSelected()); if (chb.isSelected()) { minmax.put(type,
- * null); } else { minmax.put(type, typeMinMax); } }
- *
- * }); men.add(chb);
- */
- if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
- {
- // graduated colourschemes for those where minmax exists for the
- // positional features
- JMenuItem mxcol = new JMenuItem(
- (typeCol instanceof Color) ? "Graduated Colour"
- : "Single Colour");
- men.add(mxcol);
- mxcol.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- if (typeCol instanceof Color)
- {
- new FeatureColourChooser(me, type);
- // write back the current colour object to update the table
- check.updateColor(fr.getFeatureStyle(type));
- }
- else
- {
- new UserDefinedColours(me, check.type,
- ((GraduatedColor) typeCol));
- }
- }
-
- });
- }
- }
- this.featurePanel.add(men);
- men.show(this.featurePanel, x, y);
- }
-
- @Override
- public void discoverAllFeatureData()
- {
- if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
- {
- rebuildGroups();
-
- }
- resetTable(false);
- }
-
- /**
- * rebuilds the group panel
- */
- public void rebuildGroups()
- {
- boolean rdrw = false;
- if (groupPanel == null)
- {
- groupPanel = new JPanel();
- }
- else
- {
- rdrw = true;
- groupPanel.removeAll();
- }
- // TODO: JAL-964 - smoothly incorporate new group entries if panel already
- // displayed and new groups present
- for (String group:fr.getFeatureGroups())
- {
- boolean vis = fr.checkGroupVisibility(group, false);
- JCheckBox 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(groupItemListener);
- // note - visibility seems to correlate with displayed. ???wtf ??
- check.setVisible(vis);
- groupPanel.add(check);
- }
- if (rdrw)
- {
- groupPanel.validate();
- }
- }
- // This routine adds and removes checkboxes depending on
- // Group selection states
- void resetTable(boolean groupsChanged)
- {
- SequenceFeature[] tmpfeatures;
- String group = null, type;
- Vector visibleChecks = new Vector();
- AlignmentI alignment = av.getAlignment();
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
-
- tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
- {
- group = tmpfeatures[index].featureGroup;
-
- if (group == null || fr.checkGroupVisibility(group, true))
- {
- type = tmpfeatures[index].getType();
- if (!visibleChecks.contains(type))
- {
- visibleChecks.addElement(type);
- }
- }
- index++;
- }
- }
-
- Component[] comps;
- int cSize = featurePanel.getComponentCount();
- MyCheckbox check;
- // This will remove any checkboxes which shouldn't be
- // visible
- for (int i = 0; i < cSize; i++)
- {
- comps = featurePanel.getComponents();
- check = (MyCheckbox) comps[i];
- if (!visibleChecks.contains(check.type))
- {
- featurePanel.remove(i);
- cSize--;
- i--;
- }
- }
-
- if (fr.getRenderOrder() != null)
- {
- // First add the checks in the previous render order,
- // in case the window has been closed and reopened
- List<String> rol = fr.getRenderOrder();
- for (int ro = rol.size() - 1; ro > -1; ro--)
- {
- String item = rol.get(ro);
-
- if (!visibleChecks.contains(item))
- {
- continue;
- }
-
- visibleChecks.removeElement(item);
-
- addCheck(false, item);
- }
- }
-
- // now add checkboxes which should be visible,
- // if they have not already been added
- Enumeration en = visibleChecks.elements();
-
- while (en.hasMoreElements())
- {
- addCheck(groupsChanged, en.nextElement().toString());
- }
-
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
- 1, 10, 5));
- featurePanel.validate();
-
- if (scrollPane != null)
- {
- scrollPane.validate();
- }
-
- itemStateChanged(null);
- }
-
- /**
- * update the checklist of feature types with the given type
- *
- * @param groupsChanged
- * true means if the type is not in the display list then it will be
- * added and displayed
- * @param type
- * feature type to be checked for in the list.
- */
- void addCheck(boolean groupsChanged, String type)
- {
- boolean addCheck;
- Component[] comps = featurePanel.getComponents();
- MyCheckbox check;
- addCheck = true;
- for (int i = 0; i < featurePanel.getComponentCount(); i++)
- {
- check = (MyCheckbox) comps[i];
- if (check.type.equals(type))
- {
- addCheck = false;
- break;
- }
- }
-
- if (addCheck)
- {
- boolean selected = false;
- if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
- {
- selected = true;
- }
-
- check = new MyCheckbox(
- type,
- selected,
- (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
- fr.getFeatureStyle(type));
-
- check.addMouseListener(this);
- check.addMouseMotionListener(this);
- check.addItemListener(this);
- if (groupsChanged)
- {
- // add at beginning of stack.
- featurePanel.add(check, 0);
- }
- else
- {
- // add at end of stack.
- featurePanel.add(check);
- }
- }
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- for (int i = 0; i < featurePanel.getComponentCount(); i++)
- {
- JCheckBox check = (JCheckBox) featurePanel.getComponent(i);
- check.setSelected(!check.isSelected());
- }
- selectionChanged();
- }
-
- private ItemListener groupItemListener = new ItemListener() {
- public void itemStateChanged(ItemEvent evt) {
- JCheckBox source = (JCheckBox) evt.getSource();
- fr.setGroupVisibility(source.getLabel(),
- source.isSelected());
- ap.seqPanel.seqCanvas.repaint();
- if (ap.overviewPanel != null)
- {
- ap.overviewPanel.updateOverviewImage();
- }
- resetTable(true);
- return;
- };
- };
- public void itemStateChanged(ItemEvent evt)
- {
- selectionChanged();
- }
-
- void selectionChanged()
- {
- Component[] comps = featurePanel.getComponents();
- int cSize = comps.length;
-
- Object[][] tmp = new Object[cSize][3];
- int tmpSize = 0;
- for (int i = 0; i < cSize; i++)
- {
- MyCheckbox check = (MyCheckbox) comps[i];
- tmp[tmpSize][0] = check.type;
- tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
- tmp[tmpSize][2] = new Boolean(check.isSelected());
- tmpSize++;
- }
-
- Object[][] data = new Object[tmpSize][3];
- System.arraycopy(tmp, 0, data, 0, tmpSize);
-
- fr.setFeaturePriority(data);
-
- ap.paintAlignment(true);
- }
-
- MyCheckbox selectedCheck;
-
- 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();
- }
- }
-
- }
-
- public void mouseDragged(MouseEvent evt)
- {
- if (((Component) evt.getSource()).getParent() != featurePanel)
- {
- return;
- }
- dragging = true;
- }
-
- public void mouseReleased(MouseEvent evt)
- {
- if (((Component) evt.getSource()).getParent() != featurePanel)
- {
- return;
- }
-
- Component comp = null;
- JCheckBox target = null;
-
- int height = evt.getY() + evt.getComponent().getLocation().y;
-
- if (height > featurePanel.getSize().height)
- {
-
- comp = featurePanel
- .getComponent(featurePanel.getComponentCount() - 1);
- }
- else if (height < 0)
- {
- comp = featurePanel.getComponent(0);
- }
- else
- {
- comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
- + evt.getComponent().getLocation().y);
- }
-
- if (comp != null && comp instanceof JCheckBox)
- {
- target = (JCheckBox) comp;
- }
-
- if (selectedCheck != null && target != null && selectedCheck != target)
- {
- int targetIndex = -1;
- for (int i = 0; i < featurePanel.getComponentCount(); i++)
- {
- if (target == featurePanel.getComponent(i))
- {
- targetIndex = i;
- break;
- }
- }
-
- featurePanel.remove(selectedCheck);
- featurePanel.add(selectedCheck, targetIndex);
- featurePanel.validate();
- itemStateChanged(null);
- }
- }
-
- public void setUserColour(String feature, Object originalColour)
- {
- if (originalColour instanceof Color
- || originalColour instanceof GraduatedColor)
- {
- fr.setColour(feature, originalColour);
- }
- else
- {
- throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
- }
- refreshTable();
- }
-
- public void refreshTable()
- {
- featurePanel.removeAll();
- resetTable(false);
- ap.paintAlignment(true);
- }
-
- public void mouseEntered(MouseEvent evt)
- {
- }
-
- public void mouseExited(MouseEvent evt)
- {
- }
-
- public void mouseClicked(MouseEvent evt)
- {
- MyCheckbox check = (MyCheckbox) evt.getSource();
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
- {
- this.popupSort(check, fr.getMinMax(), 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("|")));
- }
- }
-
- if (check.getParent() != featurePanel)
- {
- return;
- }
-
- if (evt.getClickCount() > 1)
- {
- Object fcol = fr.getFeatureStyle(check.type);
- if (fcol instanceof Color)
- {
- new UserDefinedColours(this, check.type, (Color) fcol);
- }
- else
- {
- new FeatureColourChooser(this, check.type);
- // write back the current colour object to update the table
- check.updateColor(fr.getFeatureStyle(check.type));
- }
- }
- }
-
- public void mouseMoved(MouseEvent evt)
- {
- }
-
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- fr.setTransparency((100 - transparency.getValue()) / 100f);
- ap.seqPanel.seqCanvas.repaint();
-
- }
-
- class MyCheckbox extends JCheckBox
- {
- public String type;
-
- public int stringWidth;
-
- boolean hasLink;
-
- GraduatedColor gcol;
-
- Color col;
-
- public void updateColor(Object newcol)
- {
- if (newcol instanceof Color)
- {
- col = (Color) newcol;
- gcol = null;
- }
- else if (newcol instanceof GraduatedColor)
- {
- gcol = (GraduatedColor) newcol;
- col = null;
- }
- else
- {
- throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
- }
- if (col != null)
- {
- setBackground(col);
- }
- else
- {
- String vlabel = type;
- if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- vlabel += " "
- + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
- : "(<)");
- }
- if (gcol.isColourByLabel())
- {
- setBackground(Color.white);
- vlabel += " (by Label)";
- }
- else
- {
- setBackground(gcol.getMinColor());
- }
- this.setLabel(vlabel);
- }
- repaint();
- }
-
- public MyCheckbox(String label, boolean checked, boolean haslink)
- {
- super(label, checked);
- type = label;
- FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
- stringWidth = fm.stringWidth(label);
- this.hasLink = haslink;
- }
-
- public MyCheckbox(String type, boolean selected, boolean b,
- Object featureStyle)
- {
- this(type, selected, b);
- updateColor(featureStyle);
- }
-
- public void paint(Graphics g)
- {
- Dimension d = getSize();
- if (gcol != null)
- {
- if (gcol.isColourByLabel())
- {
- g.setColor(Color.white);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
- /*
- * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
- * g.setFont(f);
- *
- * // g.setFont(g.getFont().deriveFont( //
- * AffineTransform.getScaleInstance( //
- * width/g.getFontMetrics().stringWidth("Label"), //
- * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
- * width/2, 0);
- */
-
- }
- else
- {
- Color maxCol = gcol.getMaxColor();
- g.setColor(maxCol);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
-
- }
- }
-
- if (hasLink)
- {
- g.drawImage(linkImage, stringWidth + 25,
- (getSize().height - linkImage.getHeight(this)) / 2, this);
- }
- }
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.api.FeatureSettingsControllerI;\r
+import jalview.bin.JalviewLite;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.schemes.AnnotationColourGradient;\r
+import jalview.schemes.GraduatedColor;\r
+import jalview.util.MessageManager;\r
+\r
+import java.awt.BorderLayout;\r
+import javax.swing.JButton;\r
+import javax.swing.JCheckBox;\r
+import java.awt.Color;\r
+import java.awt.Component;\r
+import java.awt.Dimension;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import javax.swing.JFrame;\r
+import java.awt.Graphics;\r
+import java.awt.GridLayout;\r
+import java.awt.Image;\r
+import javax.swing.JLabel;\r
+import javax.swing.JMenuItem;\r
+import javax.swing.JPanel;\r
+import javax.swing.JPopupMenu;\r
+import javax.swing.JScrollPane;\r
+import javax.swing.JScrollBar;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.AdjustmentEvent;\r
+import java.awt.event.AdjustmentListener;\r
+import java.awt.event.InputEvent;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.event.MouseListener;\r
+import java.awt.event.MouseMotionListener;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.List;\r
+import java.util.Vector;\r
+\r
+public class FeatureSettings extends JPanel implements ItemListener,\r
+ MouseListener, MouseMotionListener, ActionListener,\r
+ AdjustmentListener, FeatureSettingsControllerI\r
+{\r
+ FeatureRenderer fr;\r
+\r
+ AlignmentPanel ap;\r
+\r
+ AlignViewport av;\r
+\r
+ JFrame frame;\r
+\r
+ JPanel groupPanel;\r
+\r
+ JPanel featurePanel = new JPanel();\r
+\r
+ JScrollPane scrollPane;\r
+\r
+ Image linkImage;\r
+\r
+ JScrollBar transparency;\r
+\r
+ public FeatureSettings(final AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ this.av = ap.av;\r
+ ap.av.featureSettings = this;\r
+ fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
+\r
+ transparency = new JScrollBar(JScrollBar.HORIZONTAL,\r
+ 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);\r
+\r
+ if (fr.isTransparencyAvailable())\r
+ {\r
+ transparency.addAdjustmentListener(this);\r
+ }\r
+ else\r
+ {\r
+ transparency.setEnabled(false);\r
+ }\r
+\r
+ java.net.URL url = getClass().getResource("/images/link.gif");\r
+ if (url != null)\r
+ {\r
+ linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);\r
+ }\r
+\r
+ if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())\r
+ {\r
+ fr.findAllFeatures(true); // was default - now true to make all visible\r
+ }\r
+\r
+ discoverAllFeatureData();\r
+\r
+ this.setLayout(new BorderLayout());\r
+ scrollPane = new JScrollPane();\r
+ scrollPane.add(featurePanel);\r
+ if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)\r
+ {\r
+ add(scrollPane, BorderLayout.CENTER);\r
+ }\r
+\r
+ JButton invert = new JButton("Invert Selection");\r
+ invert.addActionListener(this);\r
+\r
+ JPanel lowerPanel = new JPanel(new GridLayout(2, 1, 5, 10));\r
+ lowerPanel.add(invert);\r
+\r
+ JPanel tPanel = new JPanel(new BorderLayout());\r
+ \r
+ if (fr.isTransparencyAvailable())\r
+ {\r
+ tPanel.add(transparency, BorderLayout.CENTER);\r
+ tPanel.add(new JLabel("Transparency"), BorderLayout.EAST);\r
+ }\r
+ else\r
+ {\r
+ tPanel.add(\r
+ new JLabel("Transparency not available in this web browser"),\r
+ BorderLayout.CENTER);\r
+ }\r
+\r
+ lowerPanel.add(tPanel, BorderLayout.SOUTH);\r
+\r
+ add(lowerPanel, BorderLayout.SOUTH);\r
+\r
+ if (groupPanel != null)\r
+ {\r
+ groupPanel\r
+ .setLayout(new GridLayout(\r
+ (fr.getFeatureGroupsSize()) / 4 + 1,\r
+ 4)); // JBPNote - this was scaled on number of visible groups. seems broken\r
+ groupPanel.validate();\r
+\r
+ add(groupPanel, BorderLayout.NORTH);\r
+ }\r
+ frame = new JFrame();\r
+ frame.add(this);\r
+ final FeatureSettings me = this;\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ if (me.av.featureSettings == me)\r
+ {\r
+ me.av.featureSettings = null;\r
+ me.ap = null;\r
+ me.av = null;\r
+ }\r
+ }\r
+ });\r
+ int height = featurePanel.getComponentCount() * 50 + 60;\r
+\r
+ height = Math.max(200, height);\r
+ height = Math.min(400, height);\r
+ int width = 300;\r
+ JalviewLite.addFrame(frame,\r
+ MessageManager.getString("label.feature_settings"), width,\r
+ height);\r
+ }\r
+\r
+ public void paint(Graphics g)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.drawString(MessageManager\r
+ .getString("label.no_features_added_to_this_alignment"), 10, 20);\r
+ g.drawString(MessageManager\r
+ .getString("label.features_can_be_added_from_searches_1"), 10,\r
+ 40);\r
+ g.drawString(MessageManager\r
+ .getString("label.features_can_be_added_from_searches_2"), 10,\r
+ 60);\r
+ }\r
+\r
+ protected void popupSort(final MyCheckbox check, final Hashtable minmax,\r
+ int x, int y)\r
+ {\r
+ final String type = check.type;\r
+ final Object typeCol = fr.getFeatureStyle(type);\r
+ JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(\r
+ "label.settings_for_type", new String[]\r
+ { type }));\r
+ JMenuItem scr = new JMenuItem(\r
+ MessageManager.getString("label.sort_by_score"));\r
+ men.add(scr);\r
+ final FeatureSettings me = this;\r
+ scr.addActionListener(new ActionListener()\r
+ {\r
+\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]\r
+ { type });\r
+ }\r
+\r
+ });\r
+ JMenuItem dens = new JMenuItem(\r
+ MessageManager.getString("label.sort_by_density"));\r
+ dens.addActionListener(new ActionListener()\r
+ {\r
+\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]\r
+ { type });\r
+ }\r
+\r
+ });\r
+ men.add(dens);\r
+ if (minmax != null)\r
+ {\r
+ final Object typeMinMax = minmax.get(type);\r
+ /*\r
+ * final java.awt.CheckboxMenuItem chb = new\r
+ * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the\r
+ * moment chb.setState(minmax.get(type) != null);\r
+ * chb.addActionListener(new ActionListener() {\r
+ * \r
+ * public void actionPerformed(ActionEvent e) {\r
+ * chb.setState(chb.isSelected()); if (chb.isSelected()) { minmax.put(type,\r
+ * null); } else { minmax.put(type, typeMinMax); } }\r
+ * \r
+ * }); men.add(chb);\r
+ */\r
+ if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)\r
+ {\r
+ // graduated colourschemes for those where minmax exists for the\r
+ // positional features\r
+ JMenuItem mxcol = new JMenuItem(\r
+ (typeCol instanceof Color) ? "Graduated Colour"\r
+ : "Single Colour");\r
+ men.add(mxcol);\r
+ mxcol.addActionListener(new ActionListener()\r
+ {\r
+\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ if (typeCol instanceof Color)\r
+ {\r
+ new FeatureColourChooser(me, type);\r
+ // write back the current colour object to update the table\r
+ check.updateColor(fr.getFeatureStyle(type));\r
+ }\r
+ else\r
+ {\r
+ new UserDefinedColours(me, check.type,\r
+ ((GraduatedColor) typeCol));\r
+ }\r
+ }\r
+\r
+ });\r
+ }\r
+ }\r
+ this.featurePanel.add(men);\r
+ men.show(this.featurePanel, x, y);\r
+ }\r
+\r
+ @Override\r
+ public void discoverAllFeatureData()\r
+ {\r
+ if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)\r
+ {\r
+ rebuildGroups();\r
+\r
+ }\r
+ resetTable(false);\r
+ }\r
+\r
+ /**\r
+ * rebuilds the group panel\r
+ */\r
+ public void rebuildGroups()\r
+ {\r
+ boolean rdrw = false;\r
+ if (groupPanel == null)\r
+ {\r
+ groupPanel = new JPanel();\r
+ }\r
+ else\r
+ {\r
+ rdrw = true;\r
+ groupPanel.removeAll();\r
+ }\r
+ // TODO: JAL-964 - smoothly incorporate new group entries if panel already\r
+ // displayed and new groups present\r
+ for (String group:fr.getFeatureGroups())\r
+ {\r
+ boolean vis = fr.checkGroupVisibility(group, false);\r
+ JCheckBox check = new MyCheckbox(group, vis,\r
+ (fr.featureLinks != null && fr.featureLinks\r
+ .containsKey(group)));\r
+ check.addMouseListener(this);\r
+ check.setFont(new Font("Serif", Font.BOLD, 12));\r
+ check.addItemListener(groupItemListener);\r
+ // note - visibility seems to correlate with displayed. ???wtf ??\r
+ check.setVisible(vis);\r
+ groupPanel.add(check);\r
+ }\r
+ if (rdrw)\r
+ {\r
+ groupPanel.validate();\r
+ }\r
+ }\r
+ // This routine adds and removes checkboxes depending on\r
+ // Group selection states\r
+ void resetTable(boolean groupsChanged)\r
+ {\r
+ SequenceFeature[] tmpfeatures;\r
+ String group = null, type;\r
+ Vector visibleChecks = new Vector();\r
+ AlignmentI alignment = av.getAlignment();\r
+ for (int i = 0; i < alignment.getHeight(); i++)\r
+ {\r
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ group = tmpfeatures[index].featureGroup;\r
+\r
+ if (group == null || fr.checkGroupVisibility(group, true))\r
+ {\r
+ type = tmpfeatures[index].getType();\r
+ if (!visibleChecks.contains(type))\r
+ {\r
+ visibleChecks.addElement(type);\r
+ }\r
+ }\r
+ index++;\r
+ }\r
+ }\r
+\r
+ Component[] comps;\r
+ int cSize = featurePanel.getComponentCount();\r
+ MyCheckbox check;\r
+ // This will remove any checkboxes which shouldn't be\r
+ // visible\r
+ for (int i = 0; i < cSize; i++)\r
+ {\r
+ comps = featurePanel.getComponents();\r
+ check = (MyCheckbox) comps[i];\r
+ if (!visibleChecks.contains(check.type))\r
+ {\r
+ featurePanel.remove(i);\r
+ cSize--;\r
+ i--;\r
+ }\r
+ }\r
+\r
+ if (fr.getRenderOrder() != null)\r
+ {\r
+ // First add the checks in the previous render order,\r
+ // in case the window has been closed and reopened\r
+ List<String> rol = fr.getRenderOrder();\r
+ for (int ro = rol.size() - 1; ro > -1; ro--)\r
+ {\r
+ String item = rol.get(ro);\r
+\r
+ if (!visibleChecks.contains(item))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ visibleChecks.removeElement(item);\r
+\r
+ addCheck(false, item);\r
+ }\r
+ }\r
+\r
+ // now add checkboxes which should be visible,\r
+ // if they have not already been added\r
+ Enumeration en = visibleChecks.elements();\r
+\r
+ while (en.hasMoreElements())\r
+ {\r
+ addCheck(groupsChanged, en.nextElement().toString());\r
+ }\r
+\r
+ featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),\r
+ 1, 10, 5));\r
+ featurePanel.validate();\r
+\r
+ if (scrollPane != null)\r
+ {\r
+ scrollPane.validate();\r
+ }\r
+\r
+ itemStateChanged(null);\r
+ }\r
+\r
+ /**\r
+ * update the checklist of feature types with the given type\r
+ * \r
+ * @param groupsChanged\r
+ * true means if the type is not in the display list then it will be\r
+ * added and displayed\r
+ * @param type\r
+ * feature type to be checked for in the list.\r
+ */\r
+ void addCheck(boolean groupsChanged, String type)\r
+ {\r
+ boolean addCheck;\r
+ Component[] comps = featurePanel.getComponents();\r
+ MyCheckbox check;\r
+ addCheck = true;\r
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
+ {\r
+ check = (MyCheckbox) comps[i];\r
+ if (check.type.equals(type))\r
+ {\r
+ addCheck = false;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (addCheck)\r
+ {\r
+ boolean selected = false;\r
+ if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))\r
+ {\r
+ selected = true;\r
+ }\r
+\r
+ check = new MyCheckbox(\r
+ type,\r
+ selected,\r
+ (fr.featureLinks != null && fr.featureLinks.containsKey(type)),\r
+ fr.getFeatureStyle(type));\r
+\r
+ check.addMouseListener(this);\r
+ check.addMouseMotionListener(this);\r
+ check.addItemListener(this);\r
+ if (groupsChanged)\r
+ {\r
+ // add at beginning of stack.\r
+ featurePanel.add(check, 0);\r
+ }\r
+ else\r
+ {\r
+ // add at end of stack.\r
+ featurePanel.add(check);\r
+ }\r
+ }\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
+ {\r
+ JCheckBox check = (JCheckBox) featurePanel.getComponent(i);\r
+ check.setSelected(!check.isSelected());\r
+ }\r
+ selectionChanged();\r
+ }\r
+\r
+ private ItemListener groupItemListener = new ItemListener() {\r
+ public void itemStateChanged(ItemEvent evt) {\r
+ JCheckBox source = (JCheckBox) evt.getSource();\r
+ fr.setGroupVisibility(source.getLabel(),\r
+ source.isSelected());\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ resetTable(true);\r
+ return;\r
+ };\r
+ };\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ selectionChanged();\r
+ }\r
+\r
+ void selectionChanged()\r
+ {\r
+ Component[] comps = featurePanel.getComponents();\r
+ int cSize = comps.length;\r
+\r
+ Object[][] tmp = new Object[cSize][3];\r
+ int tmpSize = 0;\r
+ for (int i = 0; i < cSize; i++)\r
+ {\r
+ MyCheckbox check = (MyCheckbox) comps[i];\r
+ tmp[tmpSize][0] = check.type;\r
+ tmp[tmpSize][1] = fr.getFeatureStyle(check.type);\r
+ tmp[tmpSize][2] = new Boolean(check.isSelected());\r
+ tmpSize++;\r
+ }\r
+\r
+ Object[][] data = new Object[tmpSize][3];\r
+ System.arraycopy(tmp, 0, data, 0, tmpSize);\r
+\r
+ fr.setFeaturePriority(data);\r
+\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ MyCheckbox selectedCheck;\r
+\r
+ boolean dragging = false;\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+\r
+ selectedCheck = (MyCheckbox) evt.getSource();\r
+\r
+ if (fr.featureLinks != null\r
+ && fr.featureLinks.containsKey(selectedCheck.type))\r
+ {\r
+ if (evt.getX() > selectedCheck.stringWidth + 20)\r
+ {\r
+ evt.consume();\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (((Component) evt.getSource()).getParent() != featurePanel)\r
+ {\r
+ return;\r
+ }\r
+ dragging = true;\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ if (((Component) evt.getSource()).getParent() != featurePanel)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Component comp = null;\r
+ JCheckBox target = null;\r
+\r
+ int height = evt.getY() + evt.getComponent().getLocation().y;\r
+\r
+ if (height > featurePanel.getSize().height)\r
+ {\r
+\r
+ comp = featurePanel\r
+ .getComponent(featurePanel.getComponentCount() - 1);\r
+ }\r
+ else if (height < 0)\r
+ {\r
+ comp = featurePanel.getComponent(0);\r
+ }\r
+ else\r
+ {\r
+ comp = featurePanel.getComponentAt(evt.getX(), evt.getY()\r
+ + evt.getComponent().getLocation().y);\r
+ }\r
+\r
+ if (comp != null && comp instanceof JCheckBox)\r
+ {\r
+ target = (JCheckBox) comp;\r
+ }\r
+\r
+ if (selectedCheck != null && target != null && selectedCheck != target)\r
+ {\r
+ int targetIndex = -1;\r
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
+ {\r
+ if (target == featurePanel.getComponent(i))\r
+ {\r
+ targetIndex = i;\r
+ break;\r
+ }\r
+ }\r
+\r
+ featurePanel.remove(selectedCheck);\r
+ featurePanel.add(selectedCheck, targetIndex);\r
+ featurePanel.validate();\r
+ itemStateChanged(null);\r
+ }\r
+ }\r
+\r
+ public void setUserColour(String feature, Object originalColour)\r
+ {\r
+ if (originalColour instanceof Color\r
+ || originalColour instanceof GraduatedColor)\r
+ {\r
+ fr.setColour(feature, originalColour);\r
+ }\r
+ else\r
+ {\r
+ throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));\r
+ }\r
+ refreshTable();\r
+ }\r
+\r
+ public void refreshTable()\r
+ {\r
+ featurePanel.removeAll();\r
+ resetTable(false);\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ MyCheckbox check = (MyCheckbox) evt.getSource();\r
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)\r
+ {\r
+ this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());\r
+ }\r
+ if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))\r
+ {\r
+ if (evt.getX() > check.stringWidth + 20)\r
+ {\r
+ evt.consume();\r
+ String link = fr.featureLinks.get(check.type).toString();\r
+ ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),\r
+ link.substring(0, link.indexOf("|")));\r
+ }\r
+ }\r
+\r
+ if (check.getParent() != featurePanel)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (evt.getClickCount() > 1)\r
+ {\r
+ Object fcol = fr.getFeatureStyle(check.type);\r
+ if (fcol instanceof Color)\r
+ {\r
+ new UserDefinedColours(this, check.type, (Color) fcol);\r
+ }\r
+ else\r
+ {\r
+ new FeatureColourChooser(this, check.type);\r
+ // write back the current colour object to update the table\r
+ check.updateColor(fr.getFeatureStyle(check.type));\r
+ }\r
+ }\r
+ }\r
+\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
+ fr.setTransparency((100 - transparency.getValue()) / 100f);\r
+ ap.seqPanel.seqCanvas.repaint();\r
+\r
+ }\r
+\r
+ class MyCheckbox extends JCheckBox\r
+ {\r
+ public String type;\r
+\r
+ public int stringWidth;\r
+\r
+ boolean hasLink;\r
+\r
+ GraduatedColor gcol;\r
+\r
+ Color col;\r
+\r
+ public void updateColor(Object newcol)\r
+ {\r
+ if (newcol instanceof Color)\r
+ {\r
+ col = (Color) newcol;\r
+ gcol = null;\r
+ }\r
+ else if (newcol instanceof GraduatedColor)\r
+ {\r
+ gcol = (GraduatedColor) newcol;\r
+ col = null;\r
+ }\r
+ else\r
+ {\r
+ throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));\r
+ }\r
+ if (col != null)\r
+ {\r
+ setBackground(col);\r
+ }\r
+ else\r
+ {\r
+ String vlabel = type;\r
+ if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ vlabel += " "\r
+ + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"\r
+ : "(<)");\r
+ }\r
+ if (gcol.isColourByLabel())\r
+ {\r
+ setBackground(Color.white);\r
+ vlabel += " (by Label)";\r
+ }\r
+ else\r
+ {\r
+ setBackground(gcol.getMinColor());\r
+ }\r
+ this.setLabel(vlabel);\r
+ }\r
+ repaint();\r
+ }\r
+\r
+ public MyCheckbox(String label, boolean checked, boolean haslink)\r
+ {\r
+ super(label, checked);\r
+ type = label;\r
+ FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());\r
+ stringWidth = fm.stringWidth(label);\r
+ this.hasLink = haslink;\r
+ }\r
+\r
+ public MyCheckbox(String type, boolean selected, boolean b,\r
+ Object featureStyle)\r
+ {\r
+ this(type, selected, b);\r
+ updateColor(featureStyle);\r
+ }\r
+\r
+ public void paint(Graphics g)\r
+ {\r
+ Dimension d = getSize();\r
+ if (gcol != null)\r
+ {\r
+ if (gcol.isColourByLabel())\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);\r
+ /*\r
+ * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);\r
+ * g.setFont(f);\r
+ * \r
+ * // g.setFont(g.getFont().deriveFont( //\r
+ * AffineTransform.getScaleInstance( //\r
+ * width/g.getFontMetrics().stringWidth("Label"), //\r
+ * height/g.getFontMetrics().getHeight()))); g.drawString("Label",\r
+ * width/2, 0);\r
+ */\r
+\r
+ }\r
+ else\r
+ {\r
+ Color maxCol = gcol.getMaxColor();\r
+ g.setColor(maxCol);\r
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);\r
+\r
+ }\r
+ }\r
+\r
+ if (hasLink)\r
+ {\r
+ g.drawImage(linkImage, stringWidth + 25,\r
+ (getSize().height - linkImage.getHeight(this)) / 2, this);\r
+ }\r
+ }\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff