-\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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.gui;\r
\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
+import jalview.datamodel.*;\r
+\r
import java.awt.*;\r
+import java.awt.event.*;\r
import java.awt.image.*;\r
-import jalview.datamodel.*;\r
\r
-public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener\r
+import javax.swing.*;\r
+\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AnnotationLabels extends JPanel implements MouseListener,\r
+ MouseMotionListener, ActionListener\r
{\r
- boolean active = false;\r
- Image image;\r
- AlignmentPanel ap ;\r
- boolean resizing = false;\r
- int oldY, mouseX;\r
- static String ADDNEW = "Add new row";\r
- static String HIDE = "Hide this row";\r
- static String DELETE = "Delete this row";\r
- static String SHOWALL="Show all hidden rows";\r
- int selectedRow = 0;\r
- int scrollOffset = 0;\r
-\r
- public AnnotationLabels(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
-\r
- java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
- Image temp = null;\r
- if (url != null)\r
- temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
-\r
- try\r
+ static String ADDNEW = "Add New Row";\r
+ static String HIDE = "Hide This Row";\r
+ static String DELETE = "Delete This Row";\r
+ static String SHOWALL = "Show All Hidden Rows";\r
+ static String OUTPUT_TEXT = "Export Annotation";\r
+ boolean resizePanel = false;\r
+ Image image;\r
+ AlignmentPanel ap;\r
+ AlignViewport av;\r
+ boolean resizing = false;\r
+ MouseEvent dragEvent;\r
+ int oldY;\r
+ int selectedRow;\r
+ int scrollOffset = 0;\r
+ Font font = new Font("Arial", Font.PLAIN, 11);\r
+\r
+\r
+ /**\r
+ * Creates a new AnnotationLabels object.\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ */\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
+\r
+ if (url != null)\r
+ {\r
+ temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+ }\r
+\r
+ try\r
+ {\r
+ MediaTracker mt = new MediaTracker(this);\r
+ mt.addImage(temp, 0);\r
+ mt.waitForID(0);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ BufferedImage bi = new BufferedImage(temp.getHeight(this),\r
+ temp.getWidth(this), BufferedImage.TYPE_INT_RGB);\r
+ Graphics2D g = (Graphics2D) bi.getGraphics();\r
+ g.rotate(Math.toRadians(90));\r
+ g.drawImage(temp, 0, -bi.getWidth(this), this);\r
+ image = (Image) bi;\r
+\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ }\r
+\r
+ public AnnotationLabels(AlignViewport av)\r
{\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(temp, 0);\r
- mt.waitForID(0);\r
+ this.av = av;\r
}\r
- catch (Exception ex) {}\r
-\r
- BufferedImage bi = new BufferedImage(temp.getHeight(this), temp.getWidth(this),\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics2D g = (Graphics2D) bi.getGraphics();\r
- g.rotate(Math.toRadians(90));\r
- g.drawImage(temp, 0, -bi.getWidth(this), this);\r
- image = (Image) bi;\r
-\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- }\r
-\r
- public void setScrollOffset(int y)\r
- {\r
- scrollOffset = y;\r
- repaint();\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
-\r
- if(evt.getActionCommand().equals(ADDNEW))\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param y DOCUMENT ME!\r
+ */\r
+ public void setScrollOffset(int y)\r
{\r
- String label = JOptionPane.showInputDialog(this, "Label for annotation");\r
- if(label==null)\r
- label = "";\r
- ap.av.alignment.addAnnotation(new AlignmentAnnotation\r
- (label,\r
- "New description",\r
- new Annotation[ap.av.alignment.getWidth()]));\r
+ scrollOffset = y;\r
+ repaint();\r
}\r
- else if(evt.getActionCommand().equals(HIDE))\r
- {\r
- aa[selectedRow].visible = false;\r
- }\r
- else if(evt.getActionCommand().equals(DELETE))\r
- {\r
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);\r
- }\r
- else if(evt.getActionCommand().equals(SHOWALL))\r
- {\r
- for(int i=0; i<aa.length; i++)\r
- aa[i].visible = true;\r
- }\r
-\r
- ap.annotationPanel.adjustPanelHeight();\r
- ap.repaint();\r
-\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- int y = evt.getY() - scrollOffset;\r
\r
+ void getSelectedRow(int y)\r
+ {\r
+ int height = 0;\r
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
- if(aa==null || aa.length==0)\r
- {\r
- JPopupMenu pop = new JPopupMenu("Annotations");\r
- JMenuItem item = new JMenuItem(ADDNEW);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
- return;\r
- }\r
-\r
- int height = 0;\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- height += aa[i].height;\r
- if(y<height)\r
- {\r
- selectedRow = i;\r
- break;\r
- }\r
- }\r
-\r
- JPopupMenu pop = new JPopupMenu("Annotations");\r
- JMenuItem item = new JMenuItem(ADDNEW);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(HIDE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(DELETE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(SHOWALL);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- oldY = evt.getY();\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt){ active = false; repaint(); }\r
- public void mouseEntered(MouseEvent evt) { active = true; repaint();}\r
- public void mouseExited(MouseEvent evt) { active = false; repaint();}\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- active = true;\r
- Dimension d = ap.annotationScroller.getPreferredSize();\r
- int dif = evt.getY() - oldY;\r
-\r
- dif /= ap.av.charHeight;\r
- dif *= ap.av.charHeight;\r
-\r
- if(d.height-dif>20)\r
+\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ height += aa[i].height;\r
+\r
+ if (y < height)\r
+ {\r
+ selectedRow = i;\r
+\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif));\r
- d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif));\r
- ap.repaint();\r
+ int dif = 0;\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+\r
+ if (evt.getActionCommand().equals(ADDNEW))\r
+ {\r
+ String label = JOptionPane.showInputDialog(this,\r
+ "Label for annotation");\r
+\r
+ if (label == null)\r
+ {\r
+ label = "";\r
+ }\r
+\r
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,\r
+ "New description",\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
+ {\r
+ aa[selectedRow].visible = false;\r
+\r
+ if (aa[selectedRow].label.equals("Conservation"))\r
+ {\r
+ ap.av.showConservation = false;\r
+ }\r
+\r
+ if (aa[selectedRow].label.equals("Quality"))\r
+ {\r
+ ap.av.showQuality = false;\r
+ }\r
+\r
+ if (aa[selectedRow].label.equals("Consensus"))\r
+ {\r
+ ap.av.showIdentity = false;\r
+ }\r
+\r
+ dif = aa[selectedRow].height * -1;\r
+ }\r
+ else if (evt.getActionCommand().equals(DELETE))\r
+ {\r
+ ap.av.alignment.deleteAnnotation(aa[selectedRow]);\r
+ dif = aa[selectedRow].height * -1;\r
+ }\r
+ else if (evt.getActionCommand().equals(SHOWALL))\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ dif += aa[i].height;\r
+ aa[i].visible = true;\r
+ }\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
+ {\r
+ new AnnotationExporter().exportAnnotations(\r
+ ap,\r
+ new AlignmentAnnotation[]\r
+ {aa[selectedRow]}\r
+ );\r
+ }\r
+\r
+\r
+ ap.annotationPanel.adjustPanelHeight();\r
+ ap.annotationScroller.validate();\r
+ ap.repaint();\r
}\r
- ap.addNotify();\r
- }\r
\r
- public void mouseMoved(MouseEvent evt) {}\r
- public void mouseClicked(MouseEvent evt) {}\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ getSelectedRow(evt.getY() - scrollOffset);\r
+ oldY = evt.getY();\r
+ }\r
\r
- public void paintComponent(Graphics g1)\r
- {\r
- Graphics2D g = (Graphics2D)g1;\r
- g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ int start = selectedRow;\r
+ getSelectedRow(evt.getY() - scrollOffset);\r
+ int end = selectedRow;\r
\r
- drawComponent(g);\r
- }\r
+ if(start!=end)\r
+ {\r
+ //Swap these annotations\r
+ AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];\r
+ AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];\r
\r
- public void drawComponent(Graphics2D g)\r
- {\r
- FontMetrics fm = g.getFontMetrics(g.getFont());\r
- g.setColor(Color.white);\r
- g.fillRect(0,0, getWidth(), getHeight());\r
\r
- g.translate(0, scrollOffset);\r
- g.setColor(Color.black);\r
+ ap.av.alignment.getAlignmentAnnotation()[end] = startAA;\r
+ ap.av.alignment.getAlignmentAnnotation()[start] = endAA;\r
+ }\r
\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
- int x = 0;\r
+ resizePanel = false;\r
+ dragEvent = null;\r
+ repaint();\r
+ ap.annotationPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if(evt.getY()<10)\r
+ {\r
+ resizePanel = true;\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent evt)\r
+ { }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ dragEvent = evt;\r
+\r
+ if (resizePanel)\r
+ {\r
+ Dimension d = ap.annotationScroller.getPreferredSize();\r
+ int dif = evt.getY() - oldY;\r
+\r
+ dif /= ap.av.charHeight;\r
+ dif *= ap.av.charHeight;\r
+\r
+ if ( (d.height - dif) > 20)\r
+ {\r
+ ap.annotationScroller.setPreferredSize(new Dimension(d.width,\r
+ d.height - dif));\r
+ d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
+ ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
+ d.width, d.height - dif));\r
+ ap.repaint();\r
+ }\r
+\r
+ ap.addNotify();\r
+ }\r
+ else\r
+ repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ resizePanel = evt.getY()<10;\r
\r
- if(aa!=null)\r
- for(int i=0; i<aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
+ repaint();\r
+ }\r
\r
- x = getWidth() - fm.stringWidth(aa[i].label)-3;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ if(!SwingUtilities.isRightMouseButton(evt))\r
+ return;\r
\r
- if(aa[i].isGraph)\r
- y+=(aa[i].height/3);\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
\r
- g.drawString(aa[i].label, x, y);\r
+ if ((aa == null) || (aa.length == 0))\r
+ {\r
+ JPopupMenu pop = new JPopupMenu("Annotations");\r
+ JMenuItem item = new JMenuItem(ADDNEW);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
\r
- if(aa[i].isGraph)\r
- y+=(2*aa[i].height/3);\r
- else\r
- y+=aa[i].height;\r
- }\r
+ return;\r
+ }\r
+\r
+\r
+ JPopupMenu pop = new JPopupMenu("Annotations");\r
+ JMenuItem item = new JMenuItem(ADDNEW);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(HIDE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(DELETE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(SHOWALL);\r
+ item.addActionListener(this);\r
+ pop.add(item);\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
- if (active)\r
- {\r
- if (image != null)\r
- g.drawImage(image, 2, 0, this);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g1 DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\r
\r
- if (aa == null || aa.length<1)\r
- {\r
- g.drawString("Right click", 2, 8);\r
- g.drawString("to add annotation", 2, 18);\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(g2, width);\r
\r
- }\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\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
+\r
+ g.translate(0, scrollOffset);\r
+ g.setColor(Color.black);\r
+\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ int fontHeight = g.getFont().getSize();\r
+ int y = fontHeight;\r
+ int x = 0;\r
+ int graphExtras = 0;\r
+\r
+\r
+\r
+ if (aa != null)\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ x = width - fm.stringWidth(aa[i].label) - 3;\r
+\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
+ 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].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
+ y += aa[i].height;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (resizePanel)\r
+ {\r
+ g.drawImage(image, 2, 0 - scrollOffset, this);\r
+ }\r
+ else if (dragEvent != null)\r
+ {\r
+ g.setColor(Color.lightGray);\r
+ g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);\r
+ }\r
+\r
+\r
+ if ((aa == null) || (aa.length < 1))\r
+ {\r
+ g.drawString("Right click", 2, 8);\r
+ g.drawString("to add annotation", 2, 18);\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff