X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=a10d58bf64e3232530f7cb9b09ebbd1944a74953;hb=c77ccc33971183dba9cb66b40886a6b61fe8eaa0;hp=0213565b98f22ce005d8521630e0a8ada21f9621;hpb=6cbc1c23947d6812cf5efa36998f237f60f4cc74;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 0213565..a10d58b 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -24,8 +24,6 @@ import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
 
-import java.util.*;
-
 import javax.swing.*;
 
 
@@ -608,8 +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;
 
@@ -626,6 +624,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+            lastSS = ' ';
+            lastSSX = 0;
 
 
             if (row.graph>0)
@@ -653,14 +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;
                 }
@@ -713,9 +712,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         g.drawString(row.annotations[column].displayCharacter, x+charOffset,
                             y + iconOffset + 3);
                     }
-                    else if (((row.annotations[column - 1] == null) ||
-                            (row.annotations[column].displayCharacter != row.annotations[column -
-                            1].displayCharacter)))
+                    else if (((row.annotations[column - 1] == null)
+                              ||
+                            (!row.annotations[column].displayCharacter.equals(
+                             row.annotations[column - 1].displayCharacter))))
                     {
                         g.drawString(row.annotations[column].displayCharacter, x+charOffset,
                             y + iconOffset + 3);
@@ -725,21 +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[]
                                 {
@@ -752,22 +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;
                     }
                 }
 
@@ -778,12 +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;
 
@@ -793,8 +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[]
@@ -804,17 +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;
                 }
@@ -883,6 +881,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(sRes>aa.annotations.length)
         return;
 
+      eRes = Math.min(eRes, aa.annotations.length);
+
       int x = 0;
 
       //Adjustment for fastpaint to left
@@ -916,7 +916,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                                         new float[] { 5f, 3f }, 0f));
 
           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
+          g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
           g2.setStroke(new BasicStroke());
       }
 
@@ -963,6 +963,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(sRes>aa.annotations.length)
         return;
 
+      eRes = Math.min(eRes, aa.annotations.length);
+
       int x=0, y1, y2;
 
       float range = max - min;
@@ -977,7 +979,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                                         new float[] { 5f, 3f }, 0f));
 
           y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
+          g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
           g2.setStroke(new BasicStroke());
       }
 
@@ -988,7 +990,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       g.setColor(Color.gray);
 
-      g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);
+      g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
 
 
       int column = sRes;