From d360d66235b8e99766ace8330175bd0258a8c07c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Mar 2006 15:33:44 +0000
Subject: [PATCH] No need to hava SSX as array

---
 src/jalview/gui/AnnotationPanel.java |   49 +++++++++++++++++-----------------
 1 file changed, 24 insertions(+), 25 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index ab6d395..a10d58b 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -606,8 +606,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         int x = 0;
         int y = 0;
-        char[] lastSS = new char[aa.length];
-        int[] lastSSX = new int[aa.length];
+        char lastSS;
+        int lastSSX;
         int iconOffset = av.charHeight / 2;
         boolean validRes = false;
 
@@ -624,6 +624,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+            lastSS = ' ';
+            lastSSX = 0;
 
 
             if (row.graph>0)
@@ -651,14 +653,13 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
             int column = startRes;
             int yPos = startRes;
-            int aaMax = row.annotations.length-1;
 
             while (yPos < endRes)
             {
               if (av.hasHiddenColumns)
               {
                 column = av.getColumnSelection().adjustForHiddenColumns(yPos);
-                if (column > aaMax)
+                if (column > row.annotations.length-1)
                 {
                   break;
                 }
@@ -724,21 +725,21 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 if (row.hasIcons)
                 {
                     if (!validRes ||
-                            (row.annotations[column].secondaryStructure != lastSS[i]))
+                            (row.annotations[column].secondaryStructure != lastSS))
                     {
-                        switch (lastSS[i])
+                        switch (lastSS)
                         {
                         case 'H':
                             g.setColor(HELIX_COLOUR);
-                            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                                x - lastSSX[i], 7, 8, 8);
+                            g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+                                x - lastSSX, 7, 8, 8);
 
                             break;
 
                         case 'E':
                             g.setColor(SHEET_COLOUR);
-                            g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                                x - lastSSX[i] - 4, 7);
+                            g.fillRect(lastSSX, y + 4 + iconOffset,
+                                x - lastSSX - 4, 7);
                             g.fillPolygon(new int[] { x - 4, x - 4, x },
                                 new int[]
                                 {
@@ -751,22 +752,22 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
                         default:
                             g.setColor(Color.gray);
-                            g.fillRect(lastSSX[i], y + 6 + iconOffset,
-                                x - lastSSX[i], 2);
+                            g.fillRect(lastSSX, y + 6 + iconOffset,
+                                x - lastSSX, 2);
 
                             break;
                         }
 
                         if (validRes)
                         {
-                            lastSS[i] = row.annotations[column].secondaryStructure;
+                            lastSS = row.annotations[column].secondaryStructure;
                         }
                         else
                         {
-                            lastSS[i] = ' ';
+                            lastSS = ' ';
                         }
 
-                        lastSSX[i] = x;
+                        lastSSX = x;
                     }
                 }
 
@@ -777,12 +778,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
             if (row.hasIcons)
             {
-                switch (lastSS[i])
+                switch (lastSS)
                 {
                 case 'H':
                     g.setColor(HELIX_COLOUR);
-                    g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                        x - lastSSX[i], 7, 8, 8);
+                    g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+                        x - lastSSX, 7, 8, 8);
 
                     break;
 
@@ -792,8 +793,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     if (row.annotations[endRes] !=null
                         && row.annotations[endRes].secondaryStructure != 'E')
                     {
-                      g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                                 x - lastSSX[i] - 4, 7);
+                      g.fillRect(lastSSX, y + 4 + iconOffset,
+                                 x - lastSSX - 4, 7);
                       g.fillPolygon(new int[]
                                     {x - 4, x - 4, x},
                                     new int[]
@@ -803,17 +804,15 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                       }, 3);
                     }
                     else
-                      g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                                 x - lastSSX[i], 7);
+                      g.fillRect(lastSSX, y + 4 + iconOffset,
+                                 x - lastSSX, 7);
 
                     break;
 
-                case 'C':
-                    break;
 
                 default:
                     g.setColor(Color.gray);
-                    g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+                    g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);
 
                     break;
                 }
-- 
1.7.10.2