Selection Group rendering updated

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index ac5ff89..5afbe23 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -152,21 +152,34 @@ public class SeqCanvas
 \r
   }\r
 \r
-  public void fastPaint(int horizontal, int vertical)\r
+  int lastsr=0;\r
+  void fastPaint(int horizontal, int vertical)\r
   {\r
-    if (fastPaint || gg == null)\r
+    if ( fastPaint || gg == null)\r
     {\r
-      repaint();\r
       return;\r
     }\r
 \r
+\r
+    // Its possible on certain browsers that the call to fastpaint\r
+    // is faster than it can paint, so this check here catches\r
+    // this possibility\r
+    if(lastsr + horizontal != av.startRes)\r
+    {\r
+      horizontal = av.startRes - lastsr;\r
+    }\r
+\r
+    lastsr = av.startRes;\r
+\r
     fastPaint = true;\r
     gg.copyArea(horizontal * av.charWidth,\r
                 vertical * av.charHeight,\r
-                imgWidth,\r
-                imgHeight,\r
+                imgWidth - horizontal * av.charWidth,\r
+                imgHeight - vertical * av.charHeight,\r
                 -horizontal * av.charWidth,\r
-                    -vertical * av.charHeight);\r
+                -vertical * av.charHeight);\r
+\r
+\r
 \r
     int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,\r
         transX = 0, transY = 0;\r
@@ -424,7 +437,7 @@ public class SeqCanvas
     return annotations.adjustPanelHeight();\r
     }\r
 \r
-  synchronized public void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset)\r
+  void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset)\r
   {\r
 \r
     g.setFont(av.getFont());\r
@@ -438,15 +451,12 @@ public class SeqCanvas
     nextSeq = av.alignment.getSequenceAt(i);\r
 \r
     sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes,\r
-                    (startRes - startRes) * av.charWidth,\r
-                    offset +\r
-                    (i - startSeq) * av.charHeight,\r
-                    av.charWidth, av.charHeight);\r
+                    offset + ( (i - startSeq) * av.charHeight));\r
 \r
     if (av.showSequenceFeatures)\r
     {\r
       fr.drawSequence(g, nextSeq, startRes, endRes,\r
-                      offset +(i - startSeq) * av.charHeight,\r
+                      offset + ((i - startSeq) * av.charHeight),\r
                       av.charWidth, av.charHeight);\r
     }\r
     /// Highlight search Results once all sequences have been drawn\r
@@ -466,162 +476,163 @@ public class SeqCanvas
    }\r
   }\r
 \r
-    /////////////////////////////////////\r
+  //\r
+  /////////////////////////////////////\r
+  // Now outline any areas if necessary\r
+  /////////////////////////////////////\r
+  SequenceGroup group = av.getSelectionGroup();\r
 \r
-    // Now outline any areas if necessary\r
-    /////////////////////////////////////\r
-    SequenceGroup group = av.getSelectionGroup();\r
-    java.util.Vector groups = av.alignment.getGroups();\r
+  int sx = -1;\r
+  int sy = -1;\r
+  int ex = -1;\r
+  int groupIndex = -1;\r
 \r
-    int sx = -1, sy = -1, ex = -1;\r
-    int groupIndex = -1;\r
-    if (group == null && groups.size() > 0)\r
-    {\r
-      group = (SequenceGroup) groups.elementAt(0);\r
+  if ((group == null) && (av.alignment.getGroups().size() > 0))\r
+  {\r
+      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
       groupIndex = 0;\r
-    }\r
-    if (group != null)\r
-    {\r
-        do\r
-        {\r
-            int oldY = -1;\r
-            int i = 0;\r
-            boolean inGroup = false;\r
-            int top = -1;\r
-            int bottom = -1;\r
+  }\r
 \r
-            for (i = startSeq; i < endSeq; i++)\r
-            {\r
-                sx = (group.getStartRes() - startRes) * av.charWidth;\r
-                sy = offset + ((i - startSeq) * av.charHeight);\r
-                ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
-                    1;\r
+  if ( group != null)\r
+  {\r
+      do\r
+      {\r
+          int oldY = -1;\r
+          int i = 0;\r
+          boolean inGroup = false;\r
+          int top = -1;\r
+          int bottom = -1;\r
+\r
+          for (i = startSeq; i < endSeq; i++)\r
+          {\r
+              sx = (group.getStartRes() - startRes) * av.charWidth;\r
+              sy = offset + ((i - startSeq) * av.charHeight);\r
+              ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
+                  1;\r
+\r
+              if(sx+ex<0 || sx>imgWidth)\r
+              {\r
+                continue;\r
+              }\r
 \r
-                if(sx+ex<0 || sx>imgWidth)\r
+              if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
+                      group.sequences.contains(av.alignment.getSequenceAt(\r
+                              i)))\r
+              {\r
+                if (bottom == -1)\r
                 {\r
-                  continue;\r
+                 if(i == endSeq-1 || // Dont check for i+1 if on the bottom row\r
+                  !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))\r
+\r
+                    bottom = sy + av.charHeight;\r
                 }\r
 \r
-                if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
-                        group.sequences.contains(av.alignment.getSequenceAt(\r
-                                i)))\r
+                  if (!inGroup)\r
+                  {\r
+                      if (((top == -1) && (i == 0)) ||\r
+                              !group.sequences.contains(\r
+                                  av.alignment.getSequenceAt(i - 1)))\r
+                      {\r
+                          top = sy;\r
+                      }\r
+\r
+                      oldY = sy;\r
+                      inGroup = true;\r
+\r
+                      if (group == av.getSelectionGroup())\r
+                      {\r
+                          g.setColor(Color.red);\r
+                      }\r
+                      else\r
+                      {\r
+                          g.setColor(group.getOutlineColour());\r
+                      }\r
+                  }\r
+              }\r
+              else\r
+              {\r
+                if (inGroup)\r
                 {\r
+                  if (sx >= 0 && sx < imgWidth)\r
+                    g.drawLine(sx, oldY, sx, sy);\r
 \r
-                    if (bottom == -1)\r
-                   {\r
-                     if(i == endSeq-1 || // Dont check for i+1 if on the bottom row\r
-                      !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))\r
-\r
-                        bottom = sy + av.charHeight;\r
-                    }\r
-\r
-                    if (!inGroup)\r
-                    {\r
-                        if (((top == -1) && (i == 0)) ||\r
-                                !group.sequences.contains(\r
-                                    av.alignment.getSequenceAt(i - 1)))\r
-                        {\r
-                            top = sy;\r
-                        }\r
-\r
-                        oldY = sy;\r
-                        inGroup = true;\r
-\r
-                        if (group == av.getSelectionGroup())\r
-                        {\r
-\r
-                            g.setColor(Color.red);\r
-                        }\r
-                        else\r
-                        {\r
-                            g.setColor(group.getOutlineColour());\r
-                        }\r
-                    }\r
-                }\r
-                else\r
-                {\r
-                  if (inGroup)\r
+                  if (sx + ex < imgWidth)\r
+                    g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+\r
+                  if (sx < 0)\r
                   {\r
-                    if (sx >= 0 && sx < imgWidth)\r
-                      g.drawLine(sx, oldY, sx, sy);\r
-\r
-                    if (sx + ex < imgWidth)\r
-                      g.drawLine(sx + ex, oldY, sx + ex, sy);\r
-\r
-                    if (sx < 0)\r
-                    {\r
-                      ex += sx;\r
-                      sx = 0;\r
-                    }\r
-\r
-                    if (sx + ex > imgWidth)\r
-                      ex = imgWidth;\r
-\r
-                    else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
-                      ex = (endRes - startRes + 1) * av.charWidth;\r
-\r
-                    if (top != -1)\r
-                    {\r
-                      g.drawLine(sx, top, sx + ex, top);\r
-                      top = -1;\r
-                    }\r
-\r
-                    if (bottom != -1)\r
-                    {\r
-                      g.drawLine(sx, bottom, sx + ex, bottom);\r
-                      bottom = -1;\r
-                    }\r
-\r
-                    inGroup = false;\r
-                    }\r
-                }\r
-            }\r
+                    ex += sx;\r
+                    sx = 0;\r
+                  }\r
 \r
-            if (inGroup)\r
-            {\r
-              sy = offset + ( (i - startSeq) * av.charHeight);\r
-              if (sx >= 0 && sx < imgWidth)\r
-                g.drawLine(sx, oldY, sx, sy);\r
+                  if (sx + ex > imgWidth)\r
+                    ex = imgWidth;\r
 \r
-              if (sx + ex < imgWidth)\r
-                g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+                  else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+                    ex = (endRes - startRes + 1) * av.charWidth;\r
 \r
-              if (sx < 0)\r
-              {\r
-                ex += sx;\r
-                sx = 0;\r
-              }\r
+                  if (top != -1)\r
+                  {\r
+                    g.drawLine(sx, top, sx + ex, top);\r
+                    top = -1;\r
+                  }\r
 \r
-              if (sx + ex > imgWidth)\r
-                ex = imgWidth;\r
-              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
-                ex = (endRes - startRes + 1) * av.charWidth;\r
+                  if (bottom != -1)\r
+                  {\r
+                    g.drawLine(sx, bottom, sx + ex, bottom);\r
+                    bottom = -1;\r
+                  }\r
 \r
-              if (top != -1)\r
-              {\r
-                g.drawLine(sx, top, sx + ex, top);\r
-                top = -1;\r
+                  inGroup = false;\r
+                  }\r
               }\r
+          }\r
 \r
-              if (bottom != -1)\r
-              {\r
-                g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
-                bottom = -1;\r
-              }\r
+          if (inGroup)\r
+          {\r
+            sy = offset + ( (i - startSeq) * av.charHeight);\r
+            if (sx >= 0 && sx < imgWidth)\r
+              g.drawLine(sx, oldY, sx, sy);\r
+\r
+            if (sx + ex < imgWidth)\r
+              g.drawLine(sx + ex, oldY, sx + ex, sy);\r
 \r
-                inGroup = false;\r
+            if (sx < 0)\r
+            {\r
+              ex += sx;\r
+              sx = 0;\r
             }\r
 \r
-            groupIndex++;\r
+            if (sx + ex > imgWidth)\r
+              ex = imgWidth;\r
+            else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+              ex = (endRes - startRes + 1) * av.charWidth;\r
 \r
-            if (groupIndex >= groups.size())\r
+            if (top != -1)\r
             {\r
-                break;\r
+              g.drawLine(sx, top, sx + ex, top);\r
+              top = -1;\r
             }\r
 \r
-            group = (SequenceGroup) groups.elementAt(groupIndex);\r
-        }\r
-        while (groupIndex < groups.size());\r
+            if (bottom != -1)\r
+            {\r
+              g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+              bottom = -1;\r
+            }\r
+\r
+              inGroup = false;\r
+          }\r
+\r
+          groupIndex++;\r
+\r
+          if (groupIndex >= av.alignment.getGroups().size())\r
+          {\r
+              break;\r
+          }\r
+\r
+          group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
+      }\r
+      while (groupIndex < av.alignment.getGroups().size());\r
     }\r
   }\r
 \r