boolean active = false;\r
Image image;\r
AlignmentPanel ap;\r
+ AlignViewport av;\r
boolean resizing = false;\r
int oldY;\r
int mouseX;\r
int selectedRow = 0;\r
int scrollOffset = 0;\r
+ Font font = new Font("Arial", Font.PLAIN, 11);\r
+\r
\r
/**\r
* Creates a new AnnotationLabels object.\r
public AnnotationLabels(AlignmentPanel ap)\r
{\r
this.ap = ap;\r
+ av = ap.av;\r
\r
java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
Image temp = null;\r
addMouseMotionListener(this);\r
}\r
\r
+ public AnnotationLabels(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
label = "";\r
}\r
\r
- ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,\r
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,\r
"New description",\r
- new Annotation[ap.av.alignment.getWidth()]));\r
+ new Annotation[ap.av.alignment.getWidth()]);\r
\r
+ ap.av.alignment.addAnnotation(newAnnotation);\r
+ ap.av.alignment.setAnnotationIndex(newAnnotation, 0);\r
dif = aa[aa.length - 1].height;\r
}\r
else if (evt.getActionCommand().equals(HIDE))\r
cap.setText(aa[selectedRow].toString());\r
}\r
\r
- ap.annotationPanel.adjustPanelHeight();\r
-\r
- Dimension d = ap.annotationScroller.getPreferredSize();\r
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,\r
- d.height + dif));\r
- d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,\r
- d.height + dif));\r
\r
- ap.addNotify();\r
+ ap.annotationPanel.adjustPanelHeight();\r
+ ap.annotationScroller.validate();\r
+ ap.repaint();\r
}\r
\r
/**\r
item = new JMenuItem(OUTPUT_TEXT);\r
item.addActionListener(this);\r
pop.add(item);\r
+\r
+ if (aa[selectedRow].label.equals("Consensus"))\r
+ {\r
+ pop.addSeparator();\r
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(\r
+ "Ignore Gaps In Consensus",\r
+ ap.av.getIgnoreGapsConsensus());\r
+ cbmi.addActionListener(new ActionListener()\r
+ {public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.av.setIgnoreGapsConsensus(cbmi.getState());\r
+ ap.repaint();\r
+ }\r
+ });\r
+ pop.add(cbmi);\r
+\r
+ }\r
+\r
pop.show(this, evt.getX(), evt.getY());\r
}\r
\r
*\r
* @param g1 DOCUMENT ME!\r
*/\r
- public void paintComponent(Graphics g1)\r
+ public void paintComponent(Graphics g)\r
{\r
- Graphics2D g = (Graphics2D) g1;\r
- g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+\r
+ int width = getWidth();\r
+ if(width==0)\r
+ width = ap.calculateIdWidth().width + 4;\r
+\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ if(av.antiAlias)\r
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
- drawComponent(g);\r
+ drawComponent(g2, width);\r
+\r
}\r
\r
/**\r
*\r
* @param g DOCUMENT ME!\r
*/\r
- public void drawComponent(Graphics2D g)\r
+ public void drawComponent(Graphics g, int width)\r
{\r
+ if(av.getFont().getSize()<10)\r
+ g.setFont(new Font("Arial", Font.PLAIN, av.getFont().getSize()-1));\r
+ else\r
+ g.setFont(font);\r
+\r
FontMetrics fm = g.getFontMetrics(g.getFont());\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getWidth(), getHeight());\r
g.translate(0, scrollOffset);\r
g.setColor(Color.black);\r
\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ int fontHeight = g.getFont().getSize();\r
+ int y = fontHeight;\r
int x = 0;\r
- int width = getWidth();\r
- if(width==0)\r
- width = ap.calculateIdWidth().width + 4;\r
+ int graphExtras = 0;\r
+\r
+\r
\r
if (aa != null)\r
{\r
\r
x = width - fm.stringWidth(aa[i].label) - 3;\r
\r
- if (aa[i].isGraph)\r
+ if (aa[i].graph>0)\r
{\r
+ graphExtras = y;\r
+\r
y += (aa[i].height / 3);\r
+\r
+ if(aa[i].graphGroup<0)\r
+ graphExtras = y + fontHeight;\r
}\r
\r
- g.drawString(aa[i].label, x, y);\r
+ if(aa[i].graphGroup>-1)\r
+ {\r
+ int groupSize = 0;\r
+ for (int gg = 0; gg < aa.length; gg++)\r
+ {\r
+ if (aa[gg].graphGroup == aa[i].graphGroup)\r
+ groupSize++;\r
+ }\r
+\r
+ if(groupSize * (fontHeight+8) < aa[i].height)\r
+ graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;\r
+\r
+ for(int gg=0; gg<aa.length; gg++)\r
+ {\r
+ if(aa[gg].graphGroup==aa[i].graphGroup)\r
+ {\r
+ x = width - fm.stringWidth(aa[gg].label) - 3;\r
+ g.drawString(aa[gg].label, x, graphExtras );\r
+ if(aa[gg].annotations[0]!=null)\r
+ g.setColor(aa[gg].annotations[0].colour);\r
+\r
+ g.drawLine( x, graphExtras+3,\r
+ x+fm.stringWidth(aa[gg].label),\r
+ graphExtras+3);\r
+\r
+ g.setColor(Color.black);\r
+ graphExtras += fontHeight+8;\r
+ }\r
+ }\r
+ }\r
+ else\r
+ g.drawString(aa[i].label, x, y);\r
\r
- if (aa[i].isGraph)\r
+ if (aa[i].graph>0)\r
{\r
+ /* if (aa[i].graphLines != null)\r
+ {\r
+ for (int gl = 0; gl < aa[i].graphLines.size(); gl++)\r
+ {\r
+ x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;\r
+ g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);\r
+ g.setColor(aa[i].getGraphLine(gl).colour);\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ g2.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_SQUARE,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[]\r
+ {5f, 3f}, 0f));\r
+\r
+ graphExtras += 3;\r
+\r
+ g.drawLine(x, graphExtras,\r
+ x+fm.stringWidth(aa[i].label),\r
+ graphExtras);\r
+ g2.setStroke(new BasicStroke());\r
+ }\r
+ }*/\r
y += ((2 * aa[i].height) / 3);\r
}\r
else\r
{\r
if (image != null)\r
{\r
- g.drawImage(image, 2, 0, this);\r
+ g.drawImage(image, 2, 0 - scrollOffset, this);\r
}\r
}\r
\r