/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
*/\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
import java.util.*;\r
+\r
+import java.awt.*;\r
import java.awt.event.*;\r
\r
+import jalview.datamodel.*;\r
\r
-public class FeatureSettings extends Panel implements ItemListener,\r
- MouseListener, MouseMotionListener\r
+public class FeatureSettings\r
+ extends Panel implements ItemListener,\r
+ MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
{\r
- final FeatureRenderer fr;\r
- final AlignmentPanel ap;\r
- final AlignViewport av;\r
- final Frame frame;\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(AlignViewport av, final AlignmentPanel ap)\r
+ public FeatureSettings(final AlignmentPanel ap)\r
{\r
this.ap = ap;\r
- this.av = av;\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
+ {\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.featuresDisplayed == null)\r
+ {\r
+ fr.findAllFeatures();\r
+ }\r
+\r
setTableData();\r
\r
this.setLayout(new BorderLayout());\r
scrollPane = new ScrollPane();\r
scrollPane.add(featurePanel);\r
- add(scrollPane, BorderLayout.CENTER);\r
- if(groupPanel!=null)\r
+ if (alignmentHasFeatures)\r
+ {\r
+ add(scrollPane, BorderLayout.CENTER);\r
+ }\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
+ {\r
+ tPanel.add(new Label("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.setLayout(\r
- new GridLayout(groupPanel.getComponentCount() / 4, 4));\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 ;\r
- if (height>400)\r
- height = 400;\r
+ int height = featurePanel.getComponentCount() * 50 + 60;\r
+\r
+ height = Math.max(200, height);\r
+ height = Math.min(400, height);\r
\r
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 250,\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
- if(fr.featureGroups==null)\r
+ alignmentHasFeatures = false;\r
+\r
+ if (fr.featureGroups == null)\r
+ {\r
fr.featureGroups = new Hashtable();\r
- else\r
- fr.featureGroups.clear();\r
+ }\r
\r
Vector allFeatures = new Vector();\r
+ Vector allGroups = new Vector();\r
SequenceFeature[] tmpfeatures;\r
+ String group;\r
\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
+ {\r
continue;\r
+ }\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
- && tmpfeatures[index].getFeatureGroup().length()>0\r
- && !fr.featureGroups.containsKey(tmpfeatures[index].getFeatureGroup()))\r
+ if (tmpfeatures[index].getFeatureGroup() != null)\r
{\r
- fr.featureGroups.put(tmpfeatures[index].getFeatureGroup(), new Boolean(true));\r
- if(groupPanel==null)\r
+ group = tmpfeatures[index].featureGroup;\r
+ if (!allGroups.contains(group))\r
{\r
- groupPanel = new Panel();\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
+ check.addMouseListener(this);\r
+ check.setFont(new Font("Serif", Font.BOLD, 12));\r
+ check.addItemListener(this);\r
+ groupPanel.add(check);\r
}\r
-\r
- Checkbox check = new Checkbox(tmpfeatures[index].getFeatureGroup(), true);\r
- check.setFont(new Font("Serif", Font.BOLD, 12));\r
- check.addItemListener(this);\r
- groupPanel.add(check);\r
}\r
\r
if (!allFeatures.contains(tmpfeatures[index].getType()))\r
{\r
- allFeatures.addElement(tmpfeatures[index].getType());\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
+ {\r
+ continue;\r
+ }\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
+ {\r
+ continue;\r
}\r
\r
+ visibleChecks.removeElement(item);\r
\r
- index ++;\r
+ addCheck(false, item);\r
}\r
}\r
\r
- resetTable();\r
- featurePanel.setLayout(new GridLayout(allFeatures.size(), 2, 10,5));\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(), 1,\r
+ 10, 5));\r
featurePanel.validate();\r
+\r
+ if (scrollPane != null)\r
+ {\r
+ scrollPane.validate();\r
+ }\r
+\r
+ itemStateChanged(null);\r
}\r
\r
- void resetTable()\r
+ void addCheck(boolean groupsChanged, String type)\r
{\r
- featurePanel.removeAll();\r
- Enumeration groups = fr.featureGroups.keys();\r
- SequenceFeature [] tmpfeatures;\r
- String group, type;\r
- Vector checksAdded = new Vector();\r
-\r
- while(groups.hasMoreElements())\r
- {\r
- group = groups.nextElement().toString();\r
- if ( !( (Boolean) fr.featureGroups.get(group)).booleanValue())\r
- continue;\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
- if (tmpfeatures[index].getFeatureGroup() != null &&\r
- tmpfeatures[index].getFeatureGroup().equals(group))\r
- {\r
- type = tmpfeatures[index].getType();\r
- if(!checksAdded.contains(type))\r
- {\r
- checksAdded.addElement(type);\r
- Checkbox check = new Checkbox(type, true);\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
- index++;\r
- }\r
- }\r
- }\r
- featurePanel.validate();\r
- if(scrollPane!=null)\r
- scrollPane.validate();\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 &&\r
+ 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
fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));\r
ap.seqPanel.seqCanvas.repaint();\r
if (ap.overviewPanel != null)\r
+ {\r
ap.overviewPanel.updateOverviewImage();\r
+ }\r
\r
- resetTable();\r
+ resetTable(true);\r
return;\r
}\r
}\r
+ selectionChanged();\r
+ }\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
- if(!check.getState())\r
- continue;\r
+ void selectionChanged()\r
+ {\r
+ Component[] comps = featurePanel.getComponents();\r
+ int cSize = comps.length;\r
\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
+ 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
+ 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
+ fr.setFeaturePriority(data);\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
}\r
\r
- Checkbox selectedCheck;\r
+ MyCheckbox selectedCheck;\r
boolean dragging = false;\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
- selectedCheck = (Checkbox)evt.getSource();\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
- dragging = true;\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
- Checkbox target = null;\r
+ Checkbox target = null;\r
\r
- int height = evt.getY()+evt.getComponent().getLocation().y;\r
+ int height = evt.getY() + evt.getComponent().getLocation().y;\r
\r
+ if (height > featurePanel.getSize().height)\r
+ {\r
\r
- if(height > this.getSize().height)\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
+ 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
+ if (comp != null && comp instanceof Checkbox)\r
+ {\r
+ target = (Checkbox) comp;\r
+ }\r
\r
- if (selectedCheck != null && target != null && selectedCheck != target)\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
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
{\r
- if(target==featurePanel.getComponent(i))\r
- { targetIndex = i; break; }\r
+ if (target == featurePanel.getComponent(i))\r
+ {\r
+ targetIndex = i;\r
+ break;\r
+ }\r
}\r
\r
-\r
featurePanel.remove(selectedCheck);\r
featurePanel.add(selectedCheck, targetIndex);\r
featurePanel.validate();\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
+ {}\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {}\r
+\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
+ {\r
+ return;\r
+ }\r
+\r
+ if (evt.getClickCount() > 1)\r
+ {\r
+ new UserDefinedColours(this, check.getLabel(),\r
+ fr.getColour(check.getLabel()));\r
+ }\r
+ }\r
+\r
+ public void mouseMoved(MouseEvent evt)\r
+ {}\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\r
+ 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 mouseEntered(MouseEvent evt){}\r
- public void mouseExited(MouseEvent evt){}\r
- public void mouseClicked(MouseEvent evt){}\r
- public void mouseMoved(MouseEvent evt){}\r
+ public void paint(Graphics g)\r
+ {\r
+ if (hasLink)\r
+ {\r
+ g.drawImage(linkImage, stringWidth + 25, (\r
+ getSize().height - linkImage.getHeight(this)) / 2,\r
+ this);\r
+ }\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff