+package jalview.gui;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import javax.swing.*;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import java.util.*;\r
+import java.awt.image.*;\r
+\r
+public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
+{\r
+ AlignViewport av;\r
+ AlignmentPanel ap;\r
+ int activeRow =-1;\r
+\r
+ ArrayList activeRes;\r
+ static String HELIX ="Helix";\r
+ static String SHEET ="Sheet";\r
+ static String LABEL ="Label";\r
+ static String REMOVE="Remove Annotation";\r
+ static String COLOUR="Colour";\r
+ static Color HELIX_COLOUR = Color.red.darker();\r
+ static Color SHEET_COLOUR = Color.green.darker().darker();\r
+\r
+ BufferedImage bi;\r
+\r
+\r
+\r
+ public AnnotationPanel(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ av = ap.av;\r
+ this.setLayout(null);\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ adjustPanelHeight();\r
+\r
+\r
+ ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );\r
+ }\r
+\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
+ ap.alabels.setScrollOffset( -evt.getValue() );\r
+ }\r
+\r
+ public void adjustPanelHeight()\r
+ {\r
+ // setHeight of panels\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ int height = 0;\r
+ if(aa!=null)\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if(!aa[i].visible)\r
+ continue;\r
+\r
+ aa[i].height = 0;\r
+\r
+ if(aa[i].hasText)\r
+ aa[i].height += av.charHeight;\r
+ if (aa[i].hasIcons)\r
+ aa[i].height += 16;\r
+\r
+ if (aa[i].isGraph)\r
+ aa[i].height += 50;\r
+\r
+ if(aa[i].height==0)\r
+ aa[i].height = 20;\r
+ height += aa[i].height;\r
+ }\r
+ else height=20;\r
+ this.setPreferredSize(new Dimension(1, height));\r
+\r
+ }\r
+\r
+ public void addEditableColumn(int i)\r
+ {\r
+ if(activeRow==-1)\r
+ {\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ for(int j=0; j<aa.length; j++)\r
+ if(aa[j].editable)\r
+ {\r
+ activeRow = j;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if(activeRes==null)\r
+ {\r
+ activeRes = new ArrayList();\r
+ activeRes.add(String.valueOf(i));\r
+ return;\r
+ }\r
+\r
+ activeRes.add(String.valueOf(i));\r
+\r
+ }\r
+\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ Annotation [] anot = aa[activeRow].annotations;\r
+\r
+ if(evt.getActionCommand().equals(REMOVE))\r
+ {\r
+ for(int i=0; i<activeRes.size(); i++)\r
+ {\r
+ anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
+ anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
+ }\r
+ }\r
+ else if(evt.getActionCommand().equals(LABEL))\r
+ {\r
+ String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );\r
+ if(label==null)\r
+ label = "";\r
+\r
+ if(label.length()>0 && !aa[activeRow].hasText)\r
+ aa[activeRow].hasText = true;\r
+\r
+ for(int i=0; i<activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+ if(anot[index]==null)\r
+ anot[index] = new Annotation(label, "", ' ',0);\r
+ anot[index].displayCharacter = label;\r
+ }\r
+ }\r
+ else if(evt.getActionCommand().equals(COLOUR))\r
+ {\r
+ Color col = JColorChooser.showDialog(this, "Choose foreground colour", Color.black);\r
+ for (int i = 0; i < activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+ if (anot[index] == null)\r
+ anot[index] = new Annotation("", "", ' ', 0);\r
+ anot[index].colour = col;\r
+ }\r
+ }\r
+ else // HELIX OR SHEET\r
+ {\r
+ char type = 0;\r
+ String symbol = "\u03B1";\r
+ if(evt.getActionCommand().equals(HELIX))\r
+ type = 'H';\r
+ else if(evt.getActionCommand().equals(SHEET))\r
+ {\r
+ type = 'E';\r
+ symbol = "\u03B2";\r
+ }\r
+\r
+ if(!aa[activeRow].hasIcons)\r
+ aa[activeRow].hasIcons = true;\r
+\r
+\r
+ String label = JOptionPane.showInputDialog("Enter a label for the structure?", symbol );\r
+ if(label==null)\r
+ label="";\r
+\r
+ if(label.length()>0 && !aa[activeRow].hasText)\r
+ aa[activeRow].hasText = true;\r
+\r
+ for(int i=0; i<activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation(label, "", type, 0);\r
+ }\r
+\r
+ anot[ index ].secondaryStructure = type;\r
+ anot[ index ].displayCharacter = label;\r
+ }\r
+ }\r
+\r
+ adjustPanelHeight();\r
+ activeRes = null;\r
+ repaint();\r
+ return;\r
+\r
+\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if (SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ if(activeRes==null)\r
+ return;\r
+\r
+ JPopupMenu pop = new JPopupMenu("Structure type");\r
+ JMenuItem item = new JMenuItem(HELIX);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(SHEET);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(LABEL);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(COLOUR);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(REMOVE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ return;\r
+ }\r
+\r
+\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ if(aa==null)\r
+ return;\r
+\r
+ int height = 0;\r
+ activeRow = -1;\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+ height+= aa[i].height;\r
+\r
+ if(evt.getY()<height)\r
+ {\r
+ if(!aa[i].editable)\r
+ {\r
+ activeRes = null;\r
+ continue;\r
+ }\r
+\r
+ activeRow = i;\r
+ break;\r
+ }\r
+ }\r
+\r
+\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+\r
+ if(evt.isControlDown() || evt.isAltDown())\r
+ addEditableColumn(res);\r
+\r
+ else if(evt.isShiftDown())\r
+ {\r
+\r
+ if(activeRes==null)\r
+ activeRes=new ArrayList();\r
+ else\r
+ {\r
+ int start = Integer.parseInt( activeRes.get( activeRes.size()-1 ).toString() );\r
+ int end = res;\r
+ if(end<start)\r
+ {\r
+ int temp = end;\r
+ end = start;\r
+ start = temp;\r
+ }\r
+ for(int n=start; n<=end; n++)\r
+ addEditableColumn(n);\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ activeRes = new ArrayList();\r
+ activeRes.add( String.valueOf(res) );\r
+ }\r
+\r
+ repaint();\r
+\r
+ }\r
+ public void mouseReleased(MouseEvent evt)\r
+ { }\r
+ public void mouseEntered(MouseEvent evt)\r
+ { }\r
+ public void mouseExited(MouseEvent evt)\r
+ { }\r
+ public void mouseDragged(MouseEvent evt)\r
+ { }\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ if(aa==null)\r
+ return;\r
+\r
+ int row = -1;\r
+ int height=0;\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+\r
+ if( aa[i].visible )\r
+ height += aa[i].height;\r
+\r
+ if(evt.getY()<height)\r
+ {\r
+ row = i;\r
+ break;\r
+ }\r
+ }\r
+\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ if(row>-1 && aa[row].annotations[res]!=null)\r
+ this.setToolTipText(aa[row].annotations[res].description);\r
+\r
+ }\r
+ public void mouseClicked(MouseEvent evt) {}\r
+\r
+\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ if(bi==null\r
+ || bi.getWidth()!=ap.annotationPanel.getWidth()\r
+ || bi.getHeight()!=ap.annotationPanel.getHeight())\r
+ {\r
+ bi = new BufferedImage(ap.annotationPanel.getWidth(),\r
+ ap.annotationPanel.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
+ }\r
+\r
+ drawComponent( (Graphics2D)bi.getGraphics() );\r
+ g.drawImage( bi, 0, 0, this);\r
+ }\r
+\r
+ public void drawComponent(Graphics2D g)\r
+ {\r
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ FontMetrics fm = g.getFontMetrics();\r
+ g.setFont(av.getFont());\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0,getWidth(),getHeight());\r
+\r
+ if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.drawString("Alignment has no annotations",20,15);\r
+ return;\r
+ }\r
+\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ int j, x=0, y=0;\r
+ char [] lastSS = new char[aa.length];\r
+ int [] lastSSX= new int[aa.length] ;\r
+ int iconOffset = av.charHeight/2;\r
+ boolean validRes = false;\r
+ //\u03B2 \u03B1\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+ AlignmentAnnotation row = aa[i];\r
+ if(!row.visible)\r
+ continue;\r
+\r
+ if(row.isGraph)\r
+ {\r
+ // this is so that we draw the characters below the graph\r
+ y += row.height;\r
+ if(row.hasText)\r
+ y -= av.charHeight;\r
+ }\r
+ if(row.hasText)\r
+ iconOffset = av.charHeight/2;\r
+ else\r
+ iconOffset = 0;\r
+\r
+ for(j=av.startRes; j<av.endRes+1; j++)\r
+ {\r
+ validRes = row.annotations[j]==null?false:true;\r
+\r
+ x = (j-av.getStartRes())*av.charWidth;\r
+\r
+\r
+ if(activeRow==i)\r
+ {\r
+\r
+ g.setColor(Color.red);\r
+\r
+ if(activeRes!=null)\r
+ for (int n = 0; n < activeRes.size(); n++)\r
+ {\r
+ int v = Integer.parseInt(activeRes.get(n).toString()) ;\r
+ if (v == j)\r
+ g.fillRect( (j-av.getStartRes()) * av.charWidth, y, av.charWidth, row.height);\r
+ }\r
+ }\r
+\r
+\r
+\r
+ if(validRes && row.annotations[j].displayCharacter.length()>0)\r
+ {\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[j].displayCharacter.\r
+ charAt(0))) / 2;\r
+ g.setColor( row.annotations[j].colour);\r
+ if(j==0)\r
+ {\r
+ if (row.annotations[0].secondaryStructure == 'H'\r
+ || row.annotations[0].secondaryStructure == 'E')\r
+ g.drawString(row.annotations[j].displayCharacter, x,\r
+ y + iconOffset + 2);\r
+ }\r
+ else if( (row.annotations[j].secondaryStructure=='H'\r
+ || row.annotations[j].secondaryStructure=='E') &&\r
+ (row.annotations[j-1]==null ||\r
+ row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
+\r
+ g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
+\r
+ if(!row.hasIcons)\r
+ g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
+ y + iconOffset + 2);\r
+ }\r
+\r
+ if(row.hasIcons)\r
+ if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
+ {\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
+ break;\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
+ g.fillPolygon(new int[] {x - 4, x- 4, x }\r
+ , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
+ break;\r
+ case 'C':\r
+ break;\r
+ default :\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
+ break;\r
+ }\r
+\r
+ if(validRes)\r
+ lastSS[i] = row.annotations[j].secondaryStructure;\r
+ else\r
+ lastSS[i] = ' ';\r
+ lastSSX[i] = x;\r
+ }\r
+\r
+ if (validRes && row.isGraph)\r
+ {\r
+ g.setColor(new Color(0,0,180));\r
+ int height = (int)((row.annotations[j].value / row.graphMax)*50);\r
+\r
+ if(row.windowLength>1)\r
+ {\r
+ int total =0;\r
+ for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)\r
+ {\r
+ if(i2<0 || i2>=av.alignment.getWidth())\r
+ continue;\r
+\r
+ total += row.annotations[i2].value;\r
+ }\r
+\r
+ total/=row.windowLength;\r
+ height = (int)( (total / row.graphMax) *50);\r
+\r
+ }\r
+\r
+ g.fillRect(x, y-height, av.charWidth, height );\r
+ }\r
+\r
+\r
+ }\r
+\r
+ x+=av.charWidth;\r
+\r
+ if(row.hasIcons)\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y+4+ iconOffset, x - lastSSX[i], 7, 8, 8);\r
+ break;\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4+ iconOffset, x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {x - 4, x - 4, x}\r
+ , new int[]\r
+ {y + iconOffset, y + 14+ iconOffset, y + 7+ iconOffset}\r
+ , 3);\r
+ break;\r
+ case 'C':\r
+ break;\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
+ break;\r
+\r
+ }\r
+\r
+ if(row.isGraph && row.hasText)\r
+ y+=av.charHeight;\r
+ if(!row.isGraph)\r
+ y+=aa[i].height;\r
+ }\r
+ }\r
+\r
+ // used by overview window\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0,width, y);\r
+ g.setColor(new Color(0,0,180));\r
+ int x = 0;\r
+ for(int j=0; j<aa.annotations.length; j++)\r
+ {\r
+ g.setColor(new Color(0, 0, 180));\r
+ int height = (int) ( (aa.annotations[j].value / aa.graphMax) * 50);\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ x+=av.charWidth;\r
+ }\r
+ }\r
+}\r