From 467af4486bf57121f72a3e1d3c82dc72cbfd3a6b Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 16 Aug 2017 20:53:45 +0100
Subject: [PATCH] JAL-2665 Working with hidden columns

---
 src/jalview/gui/SeqCanvas.java |   95 ++++++++++++++++++++++++++--------------
 1 file changed, 62 insertions(+), 33 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 318d74d..9bd38c5 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1073,9 +1073,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     else
     {
       // package into blocks of visible columns
-      // Graphics2D g = (Graphics2D) selectionImage.getGraphics();
-      // Graphics g1 = selectionImage.getGraphics();
-
       int screenY = 0;
       int blockStart = startRes;
       int blockEnd = endRes;
@@ -1117,7 +1114,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         g.translate(screenY * charWidth, 0);
         drawSelectionGroupPart(g, group,
                 blockStart, blockEnd, startSeq, endSeq);
-
+        
         g.translate(-screenY * charWidth, 0);
       }
     }
@@ -1157,13 +1154,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       horizontalOffset = (slice * cWidth);
     }
 
-    int visWidth = av.getRanges().getViewportWidth() * charWidth;
-
-    // set x start and end positions of group
-    int startx = (group.getStartRes() - startRes - horizontalOffset)
-            * charWidth;
-    int endx = (group.getEndRes() - startRes + 1 - horizontalOffset)
-            * charWidth;
+    int visWidth = (endRes - startRes + 1) * charWidth;
 
     int oldY = -1;
     int i = 0;
@@ -1171,13 +1162,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int top = -1;
     int bottom = -1;
 
-    // get sequences to determine y positions of group
-    for (i = startSeq; i <= endSeq; ++i)
+    int sx = -1;
+    int sy = -1;
+    int ex = -1;
+
+    // position of start residue of group relative to startRes, in pixels
+    sx = (group.getStartRes() - startRes - horizontalOffset) * charWidth;
+
+    // width of group in pixels
+    ex = (((group.getEndRes() + 1) - group.getStartRes() - horizontalOffset)
+            * charWidth) - 1;
+
+    for (i = startSeq; i <= endSeq; i++)
     {
-      int sy = verticalOffset + (i - startSeq) * charHeight;
+      sy = verticalOffset + (i - startSeq) * charHeight;
 
-      if (group.getSequences(null)
-              .contains(av.getAlignment().getSequenceAt(i)))
+      if (sx + ex < 0 || sx > visWidth)
+      {
+        continue;
+      }
+
+      if ((sx <= (endRes - startRes) * charWidth)
+              && group.getSequences(null)
+                      .contains(av.getAlignment().getSequenceAt(i)))
       {
         if ((bottom == -1) && !group.getSequences(null)
                 .contains(av.getAlignment().getSequenceAt(i + 1)))
@@ -1203,34 +1210,45 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         {
           // if start position is visible, draw vertical line to left of
           // group
-          if (startx >= 0 && startx < visWidth * charWidth)
+          if (sx >= 0 && sx < visWidth)
           {
-            g.drawLine(startx, oldY, startx, sy);
+            g.drawLine(sx, oldY, sx, sy);
           }
 
           // if end position is visible, draw vertical line to right of
           // group
-          if (endx <= visWidth * charWidth)
+          if (sx + ex < visWidth)
+          {
+            g.drawLine(sx + ex, oldY, sx + ex, sy);
+          }
+
+          if (sx < 0)
           {
-            g.drawLine(endx, oldY, endx, sy);
+            ex += sx;
+            sx = 0;
           }
 
-          if (endx > visWidth * charWidth)
+          if (sx + ex > visWidth)
           {
-            endx = visWidth * charWidth;
+            ex = visWidth;
+          }
+
+          else if (sx + ex >= (endRes - startRes + 1) * charWidth)
+          {
+            ex = (endRes - startRes + 1) * charWidth;
           }
 
           // draw horizontal line at top of group
           if (top != -1)
           {
-            g.drawLine(startx, top, endx, top);
+            g.drawLine(sx, top, sx + ex, top);
             top = -1;
           }
 
           // draw horizontal line at bottom of group
           if (bottom != -1)
           {
-            g.drawLine(startx, bottom, endx, bottom);
+            g.drawLine(sx, bottom, sx + ex, bottom);
             bottom = -1;
           }
 
@@ -1238,33 +1256,44 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         }
       }
     }
+
     if (inGroup)
     {
-      int sy = verticalOffset + (i - startSeq) * charHeight;
-      if (startx >= 0 && startx < visWidth)
+      sy = verticalOffset + ((i - startSeq) * charHeight);
+      if (sx >= 0 && sx < visWidth)
       {
-        g.drawLine(startx, oldY, startx, sy);
+        g.drawLine(sx, oldY, sx, sy);
       }
 
-      if (endx < visWidth)
+      if (sx + ex < visWidth)
       {
-        g.drawLine(endx, oldY, endx, sy);
+        g.drawLine(sx + ex, oldY, sx + ex, sy);
       }
 
-      if (endx > visWidth)
+      if (sx < 0)
+      {
+        ex += sx;
+        sx = 0;
+      }
+
+      if (sx + ex > visWidth)
+      {
+        ex = visWidth;
+      }
+      else if (sx + ex >= (endRes - startRes + 1) * charWidth)
       {
-        endx = visWidth;
+        ex = (endRes - startRes + 1) * charWidth;
       }
 
       if (top != -1)
       {
-        g.drawLine(startx, top, endx, top);
+        g.drawLine(sx, top, sx + ex, top);
         top = -1;
       }
 
       if (bottom != -1)
       {
-        g.drawLine(startx, bottom - 1, endx, bottom - 1);
+        g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
         bottom = -1;
       }
 
-- 
1.7.10.2