+ protected int offy = 4;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public int width;\r
+ protected AlignViewport av;\r
+ AlignmentPanel ap;\r
+ boolean stretchingGroup = false;\r
+ int min; //used by mouseDragged to see if user\r
+ int max; //used by mouseDragged to see if user\r
+ boolean mouseDragging = false;\r
+\r
+ // wants to delete columns\r
+ public ScalePanel(AlignViewport av, AlignmentPanel ap)\r
+ {\r
+ this.av = av;\r
+ this.ap = ap;\r
+\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ final int res;\r
+\r
+ if(av.hasHiddenColumns)\r
+ res = av.getColumnSelection().adjustForHiddenColumns(x);\r
+ else\r
+ res = x;\r
+\r
+ min = res;\r
+ max = res;\r
+\r
+ if (SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ JPopupMenu pop = new JPopupMenu();\r
+ if (reveal != null)\r
+ {\r
+ JMenuItem item = new JMenuItem("Reveal");\r
+ item.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ av.showColumn(reveal[0]);\r
+ reveal = null;\r
+ ap.repaint();\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ });\r
+ pop.add(item);\r
+\r
+ if (av.getColumnSelection().getHiddenColumns().size() > 1)\r
+ {\r
+ item = new JMenuItem("Reveal All");\r
+ item.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ av.showAllHiddenColumns();\r
+ reveal = null;\r
+ ap.repaint();\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ });\r
+ pop.add(item);\r
+ }\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ }\r
+ else if (av.getColumnSelection().contains(res))\r
+ {\r
+ JMenuItem item = new JMenuItem("Hide Columns");\r
+ item.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ av.hideColumns(res, res);\r
+ if(av.getSelectionGroup()!=null\r
+ && av.getSelectionGroup().getSize(false)==av.alignment.getHeight())\r
+ av.setSelectionGroup(null);\r
+\r
+ ap.repaint();\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ });\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ }\r
+ }\r
+ else // LEFT MOUSE TO SELECT\r
+ {\r
+ if (!evt.isControlDown() && !evt.isShiftDown())\r
+ {\r
+ av.getColumnSelection().clear();\r
+ }\r
+\r
+ av.getColumnSelection().addElement(res);\r
+ SequenceGroup sg = new SequenceGroup();\r
+ for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(av.alignment.getSequenceAt(i), false);\r
+ }\r
+\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ av.setSelectionGroup(sg);\r
+\r
+ if(evt.isShiftDown())\r
+ {\r
+ int min = Math.min(av.getColumnSelection().getMin(), res);\r
+ int max = Math.max(av.getColumnSelection().getMax(), res);\r
+ for (int i = min; i<max; i++)\r
+ {\r
+ av.getColumnSelection().addElement(i);\r
+ }\r
+ sg.setStartRes(min);\r
+ sg.setEndRes(max);\r
+ }\r
+\r
+\r
+ }\r
+\r
+\r
+ ap.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ mouseDragging = false;\r
+\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+\r
+ if(res> av.alignment.getWidth())\r
+ {\r
+ res = av.alignment.getWidth()-1;\r
+ }\r
+\r
+ if(av.hasHiddenColumns)\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+\r
+ if (!stretchingGroup)\r
+ {\r
+ ap.repaint();\r
+\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+\r
+ if(sg!=null){\r
+ if (res > sg.getStartRes())\r
+ {\r
+ sg.setEndRes(res);\r
+ }\r
+ else if (res < sg.getStartRes())\r
+ {\r
+ sg.setStartRes(res);\r
+ }\r
+ }\r
+ stretchingGroup = false;\r
+ ap.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ mouseDragging = true;\r
+\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ if(res<0)\r
+ res = 0;\r
+\r
+ if(av.hasHiddenColumns)\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+\r
+\r
+ if(res> av.alignment.getWidth())\r
+ {\r
+ res = av.alignment.getWidth()-1;\r
+ }\r
+\r
+ if (res < min)\r
+ {\r
+ min = res;\r
+ }\r