Read startgroup and endgroup in features file

[jalview.git] / src / jalview / gui / AnnotationPanel.java

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 27ac873..69ae398 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -363,20 +363,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 }\r
                 else if(aa[i].graph>0)\r
                 {\r
-                  if(SwingUtilities.isRightMouseButton(evt)\r
-                      && aa[i].graphLines!=null\r
-                       && aa[i].graphLines.size()>0)\r
-                  {\r
-                    SliderPanel sp = new SliderPanel(aa[i], ap);\r
-                    return;\r
-                  }\r
-                  else\r
-                  {\r
                     //Stretch Graph\r
                     graphStretch = i;\r
                     graphStretchY = evt.getY();\r
                     activeRes = null;\r
-                  }\r
                 }\r
                 else\r
                 {\r
@@ -862,7 +852,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 case 'E':\r
                     g.setColor(SHEET_COLOUR);\r
 \r
-                    if (row.annotations.length > endRes\r
+                    if (row.annotations[endRes] !=null\r
                         && row.annotations[endRes].secondaryStructure != 'E')\r
                     {\r
                       g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
@@ -978,21 +968,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 \r
 \r
-      if(aa.graphLines!=null)\r
+      if(aa.threshold!=null)\r
       {\r
-        for(int l=0; l<aa.graphLines.size(); l++)\r
-        {\r
-          g.setColor(aa.getGraphLine(l).colour);\r
+          g.setColor(aa.threshold.colour);\r
           Graphics2D g2 = (Graphics2D)g;\r
           g2.setStroke(new BasicStroke(1,\r
                                         BasicStroke.CAP_SQUARE,\r
                                         BasicStroke.JOIN_ROUND, 3f,\r
                                         new float[] { 5f, 3f }, 0f));\r
 \r
-          y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*graphHeight);\r
+          y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
           g2.setStroke(new BasicStroke());\r
-        }\r
       }\r
 \r
       eRes = Math.min(eRes, aa.annotations.length);\r
@@ -1023,21 +1010,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
       float range = max - min;\r
 \r
-      if(aa.graphLines!=null)\r
+      if(aa.threshold!=null)\r
       {\r
-        for(int l=0; l<aa.graphLines.size(); l++)\r
-        {\r
-          g.setColor(aa.getGraphLine(l).colour);\r
+          g.setColor(aa.threshold.colour);\r
           Graphics2D g2 = (Graphics2D)g;\r
           g2.setStroke(new BasicStroke(1,\r
                                         BasicStroke.CAP_SQUARE,\r
                                         BasicStroke.JOIN_ROUND, 3f,\r
                                         new float[] { 5f, 3f }, 0f));\r
 \r
-          y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*aa.graphHeight);\r
+          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
           g2.setStroke(new BasicStroke());\r
-        }\r
       }\r
 \r
       y1 = y2 = y;\r