/*\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) 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
\r
\r
public class FeatureSettings extends Panel implements ItemListener,\r
- MouseListener, MouseMotionListener\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
{\r
this.av = 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 = this.getComponentCount()*50;\r
- if (height>400)\r
- height = 400;\r
+ int height = featurePanel.getComponentCount()*50 +60;\r
+\r
\r
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 200,\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 features;\r
- Enumeration e;\r
- SequenceFeature sf;\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
- features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
- if (features == null)\r
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
continue;\r
\r
- e = features.elements();\r
- while (e.hasMoreElements())\r
+ alignmentHasFeatures = true;\r
+\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
{\r
- sf = (SequenceFeature) e.nextElement();\r
- if (!allFeatures.contains(sf.getType()))\r
+ if(tmpfeatures[index].getFeatureGroup()!=null)\r
{\r
- allFeatures.addElement(sf.getType());\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
- int fSize = allFeatures.size();\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
- String type;\r
- this.setLayout(new GridLayout(fSize, 2, 10,5));\r
\r
- for (int i = 0; i < fSize; i++)\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
- type = allFeatures.elementAt(i).toString();\r
- Color col = fr.getColour(type);\r
- boolean displayed = true;\r
- if(fr.featuresDisplayed!=null)\r
- displayed = fr.featuresDisplayed.contains(type);\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
- Checkbox check = new Checkbox(type, displayed);\r
check.addMouseListener(this);\r
check.addMouseMotionListener(this);\r
- check.setBackground(col);\r
+ check.setBackground(fr.getColour(type));\r
check.addItemListener(this);\r
- add(check);\r
+ featurePanel.add(check);\r
}\r
- validate();\r
}\r
\r
- public void itemStateChanged(ItemEvent evt)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
- Component [] comps = this.getComponents();\r
- int cSize = comps.length;\r
-\r
- Object [][] data = new Object[cSize][3];\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
- for(int i=0; i<cSize; i++)\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (evt != null)\r
{\r
- Checkbox check = (Checkbox)comps[i];\r
- data[i][0] = check.getLabel();\r
- data[i][1] = fr.getColour(check.getLabel());\r
- data[i][2] = new Boolean(check.getState());\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
- fr.setFeaturePriority(data);\r
- ap.seqPanel.seqCanvas.repaint();\r
- if(ap.overviewPanel!=null)\r
- ap.overviewPanel.updateOverviewImage();\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
- 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
+ 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 > this.getSize().height)\r
+ if(height > featurePanel.getSize().height)\r
{\r
- comp = this.getComponent(this.getComponentCount()-1);\r
+\r
+ comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);\r
}\r
else if(height < 0)\r
{\r
- comp = this.getComponent(0);\r
+ comp = featurePanel.getComponent(0);\r
}\r
else\r
{\r
- comp = this.getComponentAt(evt.getX(),\r
+ comp = featurePanel.getComponentAt(evt.getX(),\r
evt.getY() +\r
evt.getComponent().getLocation().y);\r
}\r
if(comp!=null && comp instanceof Checkbox)\r
target = (Checkbox)comp;\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<this.getComponentCount(); i++)\r
+ for(int i=0; i<featurePanel.getComponentCount(); i++)\r
{\r
- if(target==this.getComponent(i))\r
+ if(target==featurePanel.getComponent(i))\r
{ targetIndex = i; break; }\r
}\r
\r
-\r
- this.remove(selectedCheck);\r
- this.add(selectedCheck, targetIndex);\r
- validate();\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
+ 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
git://source.jalview.org / jalview.git / blobdiff