New class

diff --git a/src/jalview/gui/SecondaryStructurePanel.java b/src/jalview/gui/SecondaryStructurePanel.java
new file mode 100755 (executable)
index 0000000..1c8bd36
--- /dev/null
+++ b/src/jalview/gui/SecondaryStructurePanel.java
@@ -0,0 +1,194 @@
+package jalview.gui;\r
+\r
+import javax.swing.JPanel;\r
+import java.awt.event.*;\r
+import java.awt.*;\r
+import java.util.*;\r
+import javax.swing.*;\r
+import jalview.datamodel.*;\r
+\r
+public class SecondaryStructurePanel extends JPanel implements ActionListener\r
+{\r
+  AlignViewport av;\r
+  Vector structures;\r
+\r
+  SecondaryStructure amend;\r
+\r
+  public SecondaryStructurePanel(AlignViewport av)\r
+  {\r
+    this.av = av;\r
+    structures = new Vector();\r
+    setPreferredSize(new Dimension(500,30));\r
+\r
+    addMouseListener(new MouseAdapter()\r
+    {\r
+      public void mousePressed(MouseEvent evt)\r
+      { doMousePressed(evt); }\r
+      public void mouseReleased(MouseEvent evt)\r
+      { doMouseReleased(evt); }\r
+    });\r
+    addMouseMotionListener(new MouseMotionAdapter()\r
+    {\r
+      public void mouseDragged(MouseEvent evt)\r
+      { doMouseDragged(evt);  }\r
+    });\r
+  }\r
+\r
+  int startRes = 0;\r
+  int endRes = 0;\r
+  boolean amendStart = false;\r
+  boolean amendEnd = false;\r
+\r
+  public void doMousePressed(MouseEvent evt)\r
+  {\r
+    amend = null;\r
+    amendStart =false;\r
+    amendEnd = false;\r
+\r
+    startRes = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+    for(int i=0; i<structures.size(); i++)\r
+    {\r
+      SecondaryStructure ss = (SecondaryStructure) structures.get(i);\r
+      if(startRes>=ss.start && startRes<=ss.end)\r
+      {\r
+        amend = ss;\r
+        if(startRes==ss.start)\r
+          amendStart = true;\r
+\r
+        if(startRes==ss.end)\r
+          amendEnd = true;\r
+\r
+        if(evt.getClickCount()==2)\r
+        {\r
+          String label = JOptionPane.showInputDialog(this, "Amend label", "Amend label", JOptionPane.QUESTION_MESSAGE );\r
+          if(label==null)\r
+            label = "";\r
+          ss.label = label;\r
+        }\r
+        break;\r
+      }\r
+    }\r
+    repaint();\r
+\r
+  }\r
+\r
+  public void doMouseReleased(MouseEvent evt)\r
+  {\r
+    endRes = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+\r
+    if(amend!=null)\r
+    {\r
+      if(amendStart)\r
+        amend.start = endRes;\r
+      if(amendEnd)\r
+        amend.end = endRes;\r
+\r
+      amend=null;\r
+      repaint();\r
+      return;\r
+    }\r
+\r
+    endRes = evt.getX() / av.getCharWidth() + av.getStartRes();\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
+    pop.show(this, evt.getX(), evt.getY());\r
+\r
+  }\r
+\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+\r
+    int type = 0;\r
+    if(evt.getActionCommand().equals("Helix"))\r
+       type = SecondaryStructure.HELIX;\r
+    else if(evt.getActionCommand().equals("Sheet"))\r
+      type = SecondaryStructure.SHEET;\r
+\r
+    String label = JOptionPane.showInputDialog(this, "Enter a label for the structure?", "Enter label", JOptionPane.QUESTION_MESSAGE );\r
+    if(label==null)\r
+      label = "";\r
+\r
+    SecondaryStructure ss = new SecondaryStructure(startRes, endRes, type, label);\r
+    structures.add(ss);\r
+    repaint();\r
+\r
+  }\r
+\r
+  public void doMouseDragged(MouseEvent evt)\r
+  {\r
+    paintNow(getGraphics());\r
+  }\r
+\r
+  void paintNow(Graphics g)\r
+  {\r
+    g.setColor(Color.white);\r
+    g.setFont(new Font("Verdana", Font.PLAIN, 10));\r
+    g.fillRect(0,0,getWidth(),getHeight());\r
+    for(int i=0; i<structures.size(); i++)\r
+    {\r
+      SecondaryStructure ss = (SecondaryStructure)structures.get(i);\r
+\r
+\r
+      if(ss.type==SecondaryStructure.SHEET)\r
+      {\r
+        g.setColor(Color.orange);\r
+        if(ss==amend)\r
+          g.setColor(Color.red);\r
+\r
+        g.fillRect( (  ss.start - av.startRes) * av.charWidth,          4,\r
+                    (ss.end - ss.start) * av.charWidth, 7);\r
+\r
+        g.fillPolygon( new int[]{ (ss.end - av.startRes )* av.charWidth,\r
+                       ( ss.end - av.startRes )* av.charWidth,\r
+                       ( ss.end - av.startRes )* av.charWidth+7},\r
+                       new int[]{0,14,7}, 3);\r
+      }\r
+\r
+      if(ss.type==SecondaryStructure.HELIX)\r
+      {\r
+        g.setColor(Color.magenta);\r
+        if(ss==amend)\r
+          g.setColor(Color.red);\r
+        g.fillRoundRect((ss.start -av.startRes)* av.charWidth, 4,\r
+                   (ss.end - ss.start) * av.charWidth, 7, 8,8);\r
+      }\r
+\r
+\r
+\r
+      g.setColor(Color.black);\r
+\r
+      int labelWidth = g.getFontMetrics().stringWidth(ss.label);\r
+\r
+      g.drawString( ss.label,  (ss.start +(ss.end-ss.start)/2 -av.startRes)*av.charWidth - labelWidth/2, 24);\r
+    }\r
+  }\r
+\r
+  public void paintComponent(Graphics g)\r
+  {\r
+    paintNow(g);\r
+  }\r
+}\r
+\r
+class SecondaryStructure\r
+{\r
+  public static int HELIX = 1;\r
+  public static int SHEET = 2;\r
+  public String label="";\r
+  public int start= 20;\r
+  public int end  = 40;\r
+  public int type = HELIX;\r
+\r
+  public SecondaryStructure(int s, int e, int t, String l)\r
+  {\r
+    start = s; end = e; type = t; label = l;\r
+  }\r
+\r
+}\r
+\r
+\r