X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=8623872ff550697490b6fcfc3e791e57ce448e5f;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=d9f7ebbfea03fd3e837718ff80d873aa41c2ae0b;hpb=b9c2f4b60cd997cc03ab560cbf211331b3658968;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d9f7ebb..8623872 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -133,9 +133,16 @@ public class SeqCanvas extends JComponent
         ypos += av.charHeight;
 
         if(av.hasHiddenColumns)
-                startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+        {
+          startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+          endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+        }
 
-        // EAST SCALE
+        int maxwidth = av.alignment.getWidth();
+        if (av.hasHiddenColumns)
+            maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+        // WEST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
             SequenceI seq = av.alignment.getSequenceAt(i);
@@ -404,19 +411,16 @@ public class SeqCanvas extends JComponent
     public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
         int startRes)
     {
-
         AlignmentI al = av.getAlignment();
 
         FontMetrics fm = getFontMetrics(av.getFont());
 
-        int LABEL_EAST = 0;
 
         if (av.scaleRightWrapped)
         {
             LABEL_EAST = fm.stringWidth(getMask());
         }
 
-        int LABEL_WEST = 0;
 
         if (av.scaleLeftWrapped)
         {
@@ -437,14 +441,18 @@ public class SeqCanvas extends JComponent
 
         int endx;
         int ypos = hgap;
+        int maxwidth = av.alignment.getWidth();
+
+        if(av.hasHiddenColumns)
+          maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
 
-        while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+        while ((ypos <= canvasHeight) && (startRes < maxwidth))
         {
           endx = startRes + cWidth -1;
 
-          if (endx > al.getWidth())
+          if (endx > maxwidth)
           {
-            endx = al.getWidth();
+            endx = maxwidth;
           }
 
             g.setFont(av.getFont());
@@ -469,6 +477,35 @@ public class SeqCanvas extends JComponent
                 drawNorthScale(g, startRes, endx, ypos);
             }
 
+            if (av.hasHiddenColumns && av.showHiddenMarkers)
+            {
+              g.setColor(Color.blue);
+              int res;
+              for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+                   i++)
+              {
+                res = av.getColumnSelection().findHiddenRegionPosition(i) -
+                    startRes;
+
+                if (res < 0 || res > endx - startRes)
+                  continue;
+
+                gg.fillPolygon(new int[]
+                               {res * av.charWidth - av.charHeight / 4,
+                               res * av.charWidth + av.charHeight / 4,
+                               res * av.charWidth},
+                               new int[]
+                               {
+                               ypos - (av.charHeight / 2),
+                               ypos - (av.charHeight / 2),
+                               ypos - (av.charHeight / 2) + 8
+                }, 3);
+
+              }
+            }
+
+
+
             // When printing we have an extra clipped region,
             // the Printable page which we need to account for here
             Shape clip = g.getClip();
@@ -560,15 +597,14 @@ public class SeqCanvas extends JComponent
 
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-          g1.setColor(Color.blue);
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      startSeq + offset,
-                      (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      startSeq + (endSeq - startSeq) * av.charHeight + offset);
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth,
-                      startSeq + offset,
-                      (blockEnd - blockStart + 1) * av.charWidth,
-                      startSeq + (endSeq - startSeq) * av.charHeight + offset);
+          if(av.getShowHiddenMarkers())
+          {
+            g1.setColor(Color.blue);
+            g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
+                        startSeq + offset,
+                        (blockEnd - blockStart + 1) * av.charWidth - 1,
+                        startSeq + (endSeq - startSeq) * av.charHeight + offset);
+          }
 
           g1.translate( -screenY * av.charWidth, 0);
           screenY += blockEnd - blockStart + 1;
@@ -580,6 +616,7 @@ public class SeqCanvas extends JComponent
           blockEnd = blockStart + (endRes - startRes) - screenY;
           g1.translate(screenY * av.charWidth, 0);
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
           g1.translate( -screenY * av.charWidth, 0);
         }
       }
@@ -591,14 +628,11 @@ public class SeqCanvas extends JComponent
 
     //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
     // int x1, int x2, int y1, int y2, int startx, int starty,
-    void draw(Graphics g1,
+    void draw(Graphics g,
                    int startRes, int endRes,
                    int startSeq, int endSeq,
                    int offset)
    {
-
-
-      Graphics2D g = (Graphics2D) g1;
       g.setFont(av.getFont());
       sr.prepare(g, av.renderGaps);
 
@@ -616,7 +650,7 @@ public class SeqCanvas extends JComponent
 
             if (av.showSequenceFeatures)
             {
-                fr.drawSequence(g1, nextSeq, startRes, endRes,
+                fr.drawSequence(g, nextSeq, startRes, endRes,
                     offset + ((i - startSeq) * av.charHeight));
             }
 
@@ -643,6 +677,17 @@ public class SeqCanvas extends JComponent
             }
           }
 
+          if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)
+            drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+
+   }
+
+   void drawGroupsBoundaries(Graphics g1,
+                   int startRes, int endRes,
+                   int startSeq, int endSeq,
+                   int offset)
+   {
+       Graphics2D g = (Graphics2D)g1;
         //
         /////////////////////////////////////
         // Now outline any areas if necessary
@@ -683,11 +728,11 @@ public class SeqCanvas extends JComponent
                     }
 
                     if ( (sx <= (endRes-startRes)*av.charWidth) &&
-                            group.sequences.contains(av.alignment.getSequenceAt(
-                                    i)))
+                            group.getSequences(false).
+                            contains(av.alignment.getSequenceAt(i)))
                     {
                         if ((bottom == -1) &&
-                                !group.sequences.contains(
+                                !group.getSequences(false).contains(
                                     av.alignment.getSequenceAt(i + 1)))
                         {
                             bottom = sy + av.charHeight;
@@ -696,7 +741,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)
                         {
                             if (((top == -1) && (i == 0)) ||
-                                    !group.sequences.contains(
+                                    !group.getSequences(false).contains(
                                         av.alignment.getSequenceAt(i - 1)))
                             {
                                 top = sy;
@@ -802,9 +847,13 @@ public class SeqCanvas extends JComponent
                 }
 
                 group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+
+                g.setStroke(new BasicStroke());
             }
             while (groupIndex < av.alignment.getGroups().size());
+
         }
+
     }
 
     /**