-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class FeatureSettings extends Panel implements ItemListener,\r
- MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
-{\r
- FeatureRenderer fr;\r
- AlignmentPanel ap;\r
- AlignViewport av;\r
- Frame frame;\r
- Panel groupPanel;\r
- Panel featurePanel = new Panel();\r
- ScrollPane scrollPane;\r
- boolean alignmentHasFeatures = false;\r
- Image linkImage;\r
- Scrollbar transparency ;\r
-\r
- public FeatureSettings(final AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- this.av = ap.av;\r
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
-\r
- transparency = new Scrollbar(Scrollbar.HORIZONTAL,\r
- 100 - (int)(fr.transparency*100), 1, 1, 100);\r
-\r
- if(fr.transparencySetter!=null)\r
- {\r
- transparency.addAdjustmentListener(this);\r
- }\r
- else\r
- transparency.setEnabled(false);\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
-\r
- if(av.featuresDisplayed==null)\r
- fr.findAllFeatures();\r
-\r
- setTableData();\r
-\r
- this.setLayout(new BorderLayout());\r
- scrollPane = new ScrollPane();\r
- scrollPane.add(featurePanel);\r
- if (alignmentHasFeatures)\r
- add(scrollPane, BorderLayout.CENTER);\r
-\r
- Button invert = new Button("Invert Selection");\r
- invert.addActionListener(this);\r
-\r
- Panel lowerPanel = new Panel(new GridLayout(2,1,5,10));\r
- lowerPanel.add(invert);\r
-\r
- Panel tPanel = new Panel(new BorderLayout());\r
-\r
- if(fr.transparencySetter!=null)\r
- {\r
- tPanel.add(transparency, BorderLayout.CENTER);\r
- tPanel.add(new Label("Transparency"), BorderLayout.EAST);\r
- }\r
- else\r
- tPanel.add(new Label("Transparency not available in this web browser"), BorderLayout.CENTER);\r
-\r
- lowerPanel.add(tPanel, BorderLayout.SOUTH);\r
-\r
- add(lowerPanel, BorderLayout.SOUTH);\r
-\r
-\r
-\r
- if(groupPanel!=null)\r
- {\r
- groupPanel.setLayout(\r
- new GridLayout( fr.featureGroups.size() / 4 + 1, 4));\r
- groupPanel.validate();\r
-\r
- add(groupPanel, BorderLayout.NORTH);\r
- }\r
- frame = new Frame();\r
- frame.add(this);\r
- int height = featurePanel.getComponentCount()*50 +60;\r
-\r
-\r
- height = Math.max(200, height);\r
- height = Math.min(400, height);\r
-\r
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280,\r
- height);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- g.setColor(Color.black);\r
- g.drawString("No Features added to this alignment!!", 10, 20);\r
- g.drawString("(Features can be added from searches or", 10, 40);\r
- g.drawString("from Jalview / GFF features files)", 10, 60);\r
- }\r
-\r
- void setTableData()\r
- {\r
- alignmentHasFeatures = false;\r
-\r
- if(fr.featureGroups==null)\r
- fr.featureGroups = new Hashtable();\r
-\r
- Vector allFeatures = new Vector();\r
- Vector allGroups = new Vector();\r
- SequenceFeature[] tmpfeatures;\r
- String group;\r
-\r
-\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
- continue;\r
-\r
- alignmentHasFeatures = true;\r
-\r
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
- int index = 0;\r
- while (index < tmpfeatures.length)\r
- {\r
- if(tmpfeatures[index].getFeatureGroup()!=null)\r
- {\r
- group = tmpfeatures[index].featureGroup;\r
- if(!allGroups.contains(group))\r
- {\r
- allGroups.addElement(group);\r
-\r
- boolean visible = true;\r
- if (fr.featureGroups.containsKey(group))\r
- {\r
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
- }\r
-\r
- fr.featureGroups.put(group, new Boolean(visible));\r
-\r
- if (groupPanel == null)\r
- {\r
- groupPanel = new Panel();\r
- }\r
-\r
- Checkbox check = new MyCheckbox(\r
- group,\r
- visible,\r
- (fr.featureLinks!=null && fr.featureLinks.containsKey(group))\r
- );\r
-\r
-\r
- check.addMouseListener(this);\r
- check.setFont(new Font("Serif", Font.BOLD, 12));\r
- check.addItemListener(this);\r
- groupPanel.add(check);\r
- }\r
- }\r
-\r
- if (!allFeatures.contains(tmpfeatures[index].getType()))\r
- {\r
- allFeatures.addElement(tmpfeatures[index].getType());\r
- }\r
- index ++;\r
- }\r
- }\r
-\r
- resetTable(false);\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
-\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
- continue;\r
-\r
- tmpfeatures = av.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.featureGroups.get(group)==null ||\r
- ((Boolean) fr.featureGroups.get(group)).booleanValue())\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
- Checkbox 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 = (Checkbox) comps[i];\r
- if (!visibleChecks.contains(check.getLabel()))\r
- {\r
- featurePanel.remove(i);\r
- cSize --;\r
- i--;\r
- }\r
- }\r
-\r
- if(fr.renderOrder!=null)\r
- {\r
- //First add the checks in the previous render order,\r
- //in case the window has been closed and reopened\r
- for(int ro=fr.renderOrder.length-1; ro>-1; ro--)\r
- {\r
- String item = fr.renderOrder[ro];\r
-\r
- if(!visibleChecks.contains(item))\r
- continue;\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
-\r
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, 10,5));\r
- featurePanel.validate();\r
-\r
-\r
- if(scrollPane!=null)\r
- scrollPane.validate();\r
-\r
- itemStateChanged(null);\r
- }\r
-\r
- void addCheck(boolean groupsChanged, String type)\r
- {\r
- boolean addCheck;\r
- Component [] comps = featurePanel.getComponents();\r
- Checkbox check;\r
- addCheck = true;\r
- for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
- {\r
- check = (Checkbox) comps[i];\r
- if (check.getLabel().equals(type))\r
- {\r
- addCheck = false;\r
- break;\r
- }\r
- }\r
-\r
- if (addCheck)\r
- {\r
- boolean selected = false;\r
- if (groupsChanged || av.featuresDisplayed.containsKey(type))\r
- {\r
- selected = true;\r
- }\r
-\r
- check = new MyCheckbox(type,\r
- selected,\r
- (fr.featureLinks!=null && fr.featureLinks.containsKey(type))\r
- );\r
-\r
- check.addMouseListener(this);\r
- check.addMouseMotionListener(this);\r
- check.setBackground(fr.getColour(type));\r
- check.addItemListener(this);\r
- featurePanel.add(check);\r
- }\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- for(int i=0; i<featurePanel.getComponentCount(); i++)\r
- {\r
- Checkbox check = (Checkbox)featurePanel.getComponent(i);\r
- check.setState(!check.getState());\r
- }\r
- selectionChanged();\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt != null)\r
- {\r
- //Is the source a top level featureGroup?\r
- Checkbox source = (Checkbox) evt.getSource();\r
- if (fr.featureGroups.containsKey(source.getLabel()))\r
- {\r
- fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));\r
- ap.seqPanel.seqCanvas.repaint();\r
- if (ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
-\r
- resetTable(true);\r
- return;\r
- }\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
- Checkbox check = (Checkbox) comps[i];\r
- tmp[tmpSize][0] = check.getLabel();\r
- tmp[tmpSize][1] = fr.getColour(check.getLabel());\r
- tmp[tmpSize][2] = new Boolean(check.getState());\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
- ap.seqPanel.seqCanvas.repaint();\r
- if (ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
-\r
- MyCheckbox selectedCheck;\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.getLabel() )\r
- )\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
- return;\r
- dragging = true;\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if(((Component)evt.getSource()).getParent()!=featurePanel)\r
- return;\r
-\r
- Component comp = null;\r
- Checkbox target = null;\r
-\r
- int height = evt.getY()+evt.getComponent().getLocation().y;\r
-\r
- if(height > featurePanel.getSize().height)\r
- {\r
-\r
- comp = featurePanel.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(),\r
- evt.getY() +\r
- evt.getComponent().getLocation().y);\r
- }\r
-\r
- if(comp!=null && comp instanceof Checkbox)\r
- target = (Checkbox)comp;\r
-\r
- if ( selectedCheck != null\r
- && target != null\r
- && selectedCheck != target)\r
- {\r
- int targetIndex = -1;\r
- for(int i=0; i<featurePanel.getComponentCount(); i++)\r
- {\r
- if(target==featurePanel.getComponent(i))\r
- { targetIndex = i; break; }\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, Color col)\r
- {\r
- fr.setColour(feature, col);\r
- featurePanel.removeAll();\r
- resetTable(false);\r
- ap.repaint();\r
- }\r
-\r
- public void mouseEntered(MouseEvent evt){}\r
- public void mouseExited(MouseEvent evt){}\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- MyCheckbox check = (MyCheckbox) evt.getSource();\r
-\r
- if (fr.featureLinks!=null\r
- && fr.featureLinks.containsKey(check.getLabel()))\r
- {\r
- if (evt.getX() > check.stringWidth + 20)\r
- {\r
- evt.consume();\r
- String link = fr.featureLinks.get(check.getLabel()).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
- return;\r
-\r
- if(evt.getClickCount()>1)\r
- {\r
- new UserDefinedColours(this, check.getLabel(),\r
- fr.getColour(check.getLabel()));\r
- }\r
- }\r
- public void mouseMoved(MouseEvent evt){}\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);\r
- ap.seqPanel.seqCanvas.repaint();\r
-\r
- }\r
-\r
- class MyCheckbox extends Checkbox\r
- {\r
- public int stringWidth;\r
- boolean hasLink;\r
- public MyCheckbox(String label, boolean checked, boolean haslink)\r
- {\r
- super(label, checked);\r
-\r
- FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());\r
- stringWidth = fm.stringWidth(label);\r
- this.hasLink = haslink;\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- if (hasLink)\r
- g.drawImage(linkImage, stringWidth + 25,(\r
- getSize().height-linkImage.getHeight(this))/2,\r
- this);\r
- }\r
- }\r
-}\r
-\r
-\r
+/*
+ * 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.FeatureColourI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+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.Arrays;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+public class FeatureSettings extends Panel implements ItemListener,
+ MouseListener, MouseMotionListener, ActionListener,
+ AdjustmentListener, FeatureSettingsControllerI
+{
+ FeatureRenderer fr;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ Frame frame;
+
+ Panel groupPanel;
+
+ Panel featurePanel = new Panel();
+
+ ScrollPane scrollPane;
+
+ Image linkImage;
+
+ Scrollbar transparency;
+
+ public FeatureSettings(final AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ ap.av.featureSettings = this;
+ fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
+
+ transparency = new Scrollbar(Scrollbar.HORIZONTAL,
+ 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
+
+ transparency.addAdjustmentListener(this);
+
+ 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 ScrollPane();
+ scrollPane.add(featurePanel);
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
+ {
+ add(scrollPane, BorderLayout.CENTER);
+ }
+
+ Button invert = new Button("Invert Selection");
+ invert.addActionListener(this);
+
+ Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
+ lowerPanel.add(invert);
+
+ Panel tPanel = new Panel(new BorderLayout());
+
+ tPanel.add(transparency, BorderLayout.CENTER);
+ tPanel.add(new Label("Transparency"), BorderLayout.EAST);
+
+ 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 Frame();
+ frame.add(this);
+ final FeatureSettings me = this;
+ frame.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ 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;
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ width, height);
+ }
+
+ @Override
+ 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 Map<String, float[][]> minmax, int x, int y)
+ {
+ final String type = check.type;
+ final FeatureColourI typeCol = fr.getFeatureStyle(type);
+ 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()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
+ .asList(new String[] { type }));
+ }
+
+ });
+ MenuItem dens = new MenuItem(
+ MessageManager.getString("label.sort_by_density"));
+ dens.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
+ .asList(new String[] { type }));
+ }
+
+ });
+ men.add(dens);
+
+ if (minmax != null)
+ {
+ final float[][] 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.getState()); if (chb.getState()) { minmax.put(type,
+ * null); } else { minmax.put(type, typeMinMax); } }
+ *
+ * }); men.add(chb);
+ */
+ if (typeMinMax != null && typeMinMax[0] != null)
+ {
+ // graduated colourschemes for those where minmax exists for the
+ // positional features
+ MenuItem mxcol = new MenuItem(
+ (typeCol.isSimpleColour()) ? "Graduated Colour"
+ : "Single Colour");
+ men.add(mxcol);
+ mxcol.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (typeCol.isSimpleColour())
+ {
+ 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, typeCol);
+ }
+ }
+
+ });
+ }
+ }
+
+ MenuItem selectContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_containing"));
+ selectContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+ false, type);
+ }
+ });
+ men.add(selectContaining);
+
+ MenuItem selectNotContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_not_containing"));
+ selectNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+ false, type);
+ }
+ });
+ men.add(selectNotContaining);
+
+ MenuItem hideContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_containing"));
+ hideContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, true);
+ }
+ });
+ men.add(hideContaining);
+
+ MenuItem hideNotContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_not_containing"));
+ hideNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, false);
+ }
+ });
+ men.add(hideNotContaining);
+
+ 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 Panel();
+ }
+ 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);
+ Checkbox check = new MyCheckbox(group, vis, false);
+ 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<String> visibleChecks = new Vector<String>();
+ 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<String> 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, false,
+ 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);
+ }
+ }
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ Checkbox check = (Checkbox) featurePanel.getComponent(i);
+ check.setState(!check.getState());
+ }
+ selectionChanged();
+ }
+
+ private ItemListener groupItemListener = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ Checkbox source = (Checkbox) evt.getSource();
+ fr.setGroupVisibility(source.getLabel(), source.getState());
+ ap.seqPanel.seqCanvas.repaint();
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ resetTable(true);
+ return;
+ };
+ };
+
+ @Override
+ 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.getState());
+ 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;
+
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (((Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+ dragging = true;
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (((Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+
+ Component comp = null;
+ Checkbox 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 Checkbox)
+ {
+ target = (Checkbox) 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, FeatureColourI originalColour)
+ {
+ fr.setColour(feature, originalColour);
+ refreshTable();
+ }
+
+ public void refreshTable()
+ {
+ featurePanel.removeAll();
+ resetTable(false);
+ ap.paintAlignment(true);
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ @Override
+ 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 (check.getParent() != featurePanel)
+ {
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ FeatureColourI fcol = fr.getFeatureStyle(check.type);
+ if (fcol.isSimpleColour())
+ {
+ new UserDefinedColours(this, check.type, fcol.getColour());
+ }
+ else
+ {
+ new FeatureColourChooser(this, check.type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(check.type));
+ }
+ }
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
+ ap.seqPanel.seqCanvas.repaint();
+
+ }
+
+ class MyCheckbox extends Checkbox
+ {
+ public String type;
+
+ public int stringWidth;
+
+ boolean hasLink;
+
+ FeatureColourI col;
+
+ public void updateColor(FeatureColourI newcol)
+ {
+ col = newcol;
+ if (col.isSimpleColour())
+ {
+ setBackground(col.getColour());
+ }
+ else
+ {
+ String vlabel = type;
+ if (col.isAboveThreshold())
+ {
+ vlabel += " (>)";
+ }
+ else if (col.isBelowThreshold())
+ {
+ vlabel += " (<)";
+ }
+ if (col.isColourByLabel())
+ {
+ setBackground(Color.white);
+ vlabel += " (by Label)";
+ }
+ else
+ {
+ setBackground(col.getMinColour());
+ }
+ 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,
+ FeatureColourI featureStyle)
+ {
+ this(type, selected, b);
+ updateColor(featureStyle);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ Dimension d = getSize();
+ if (col != null)
+ {
+ if (col.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 if (col.isGraduatedColour())
+ {
+ Color maxCol = col.getMaxColour();
+ 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);
+ }
+ }
+ }
+
+ /**
+ * Hide columns containing (or not containing) a given feature type
+ *
+ * @param type
+ * @param columnsContaining
+ */
+ void hideFeatureColumns(final String type, boolean columnsContaining)
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+ false, false, type))
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(
+ !columnsContaining, false, false, type))
+ {
+ ap.alignFrame.viewport.hideSelectedColumns();
+ }
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff