From 90b2653fcf34862d9c3d6a48eebce0428bc6e331 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Feb 2006 15:25:27 +0000
Subject: [PATCH 1/1] Threshold single element

---
 src/jalview/gui/AnnotationColourChooser.java |    4 ++--
 src/jalview/gui/AnnotationLabels.java        |    4 ++--
 src/jalview/gui/AnnotationPanel.java         |   21 +++++++--------------
 3 files changed, 11 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 06040a6..25eee10 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -221,9 +221,9 @@ public class AnnotationColourChooser
     else if(threshold.getSelectedItem().equals("Below Threshold"))
       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 
-    if(aboveThreshold!=AnnotationColourGradient.NO_THRESHOLD && aa.graphLines==null)
+    if(aboveThreshold!=AnnotationColourGradient.NO_THRESHOLD && aa.threshold==null)
    {
-     aa.addGraphLine(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));
+     aa.setThreshold(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));
    }
 
     AnnotationColourGradient acg = new AnnotationColourGradient(aa,
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 1068980..bffa89a 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -449,7 +449,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
                 if (aa[i].graph>0)
                 {
-                  if (aa[i].graphLines != null)
+                /*  if (aa[i].graphLines != null)
                   {
                     for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
                     {
@@ -470,7 +470,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                                  graphExtras);
                       g2.setStroke(new BasicStroke());
                     }
-                  }
+                  }*/
                     y += ((2 * aa[i].height) / 3);
                 }
                 else
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index f30c41c..41479aa 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -364,8 +364,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 else if(aa[i].graph>0)
                 {
                   if(SwingUtilities.isRightMouseButton(evt)
-                      && aa[i].graphLines!=null
-                       && aa[i].graphLines.size()>0)
+                      && aa[i].threshold!=null)
                   {
                     SliderPanel sp = new SliderPanel(aa[i], ap);
                     return;
@@ -978,21 +977,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
 
 
-      if(aa.graphLines!=null)
+      if(aa.threshold!=null)
       {
-        for(int l=0; l<aa.graphLines.size(); l++)
-        {
-          g.setColor(aa.getGraphLine(l).colour);
+          g.setColor(aa.threshold.colour);
           Graphics2D g2 = (Graphics2D)g;
           g2.setStroke(new BasicStroke(1,
                                         BasicStroke.CAP_SQUARE,
                                         BasicStroke.JOIN_ROUND, 3f,
                                         new float[] { 5f, 3f }, 0f));
 
-          y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*graphHeight);
+          y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
           g2.setStroke(new BasicStroke());
-        }
       }
 
       eRes = Math.min(eRes, aa.annotations.length);
@@ -1023,21 +1019,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       float range = max - min;
 
-      if(aa.graphLines!=null)
+      if(aa.threshold!=null)
       {
-        for(int l=0; l<aa.graphLines.size(); l++)
-        {
-          g.setColor(aa.getGraphLine(l).colour);
+          g.setColor(aa.threshold.colour);
           Graphics2D g2 = (Graphics2D)g;
           g2.setStroke(new BasicStroke(1,
                                         BasicStroke.CAP_SQUARE,
                                         BasicStroke.JOIN_ROUND, 3f,
                                         new float[] { 5f, 3f }, 0f));
 
-          y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*aa.graphHeight);
+          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
           g2.setStroke(new BasicStroke());
-        }
       }
 
       y1 = y2 = y;
-- 
1.7.10.2