av.showHiddenMarkers check

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index a05c6c0..5959493 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -65,8 +65,7 @@ public class IdCanvas extends JPanel
      * @param starty DOCUMENT ME!\r
      * @param ypos DOCUMENT ME!\r
      */\r
-    public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,\r
-        int ypos)\r
+    public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)\r
     {\r
         int charHeight = av.charHeight;\r
 \r
@@ -96,6 +95,11 @@ public class IdCanvas extends JPanel
 \r
         gg.drawString( s.getDisplayId(av.getShowJVSuffix()),\r
                       0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+\r
+        if (av.hasHiddenRows && av.showHiddenMarkers)\r
+          drawMarker(i, starty, ypos);\r
+\r
+\r
     }\r
 \r
     /**\r
@@ -249,7 +253,7 @@ public class IdCanvas extends JPanel
               {\r
                 if (av.hasHiddenRows)\r
                 {\r
-                  setHiddenFont(i, starty);\r
+                  setHiddenFont(i);\r
                 }\r
                 else\r
                   gg.setFont(italic);\r
@@ -264,16 +268,20 @@ public class IdCanvas extends JPanel
                   labels.drawComponent(gg, getWidth());\r
                   gg.translate(0, -ypos-(alheight * av.charHeight));\r
                 }\r
+\r
+\r
             }\r
         }\r
         else\r
         {\r
+          //Now draw the id strings\r
+\r
             //Now draw the id strings\r
             for (int i = starty; i < endy; i++)\r
             {\r
               if (av.hasHiddenRows)\r
               {\r
-                setHiddenFont(i, starty);\r
+                setHiddenFont(i);\r
               }\r
 \r
                 // Selected sequence colours\r
@@ -308,32 +316,60 @@ public class IdCanvas extends JPanel
                 gg.drawString(string, 0,\r
                     (((i - starty) * av.charHeight) + av.charHeight) -\r
                     (av.charHeight / 5));\r
+\r
+               if(av.hasHiddenRows && av.showHiddenMarkers)\r
+                 drawMarker(i, starty, 0);\r
+\r
             }\r
 \r
         }\r
     }\r
 \r
-    void setHiddenFont(int i, int starty)\r
+    void drawMarker(int i, int starty, int yoffset)\r
     {\r
-      Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
-                             av.getFont().getSize());\r
-      Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
-                           av.getFont().getSize());\r
+      int hiddenIndex = av.adjustForHiddenSeqs(i);\r
+      int lastIndex = av.adjustForHiddenSeqs(i - 1);\r
+      int nextIndex = av.adjustForHiddenSeqs(i + 1);\r
 \r
-      int tmp, hiddenIndex = starty;\r
-      tmp = av.adjustForHiddenSeqs(i);\r
+      boolean below = (hiddenIndex > lastIndex + 1);\r
+      boolean above = (nextIndex>hiddenIndex+1);\r
 \r
-      if (av.adjustForHiddenSeqs(i - 1) == tmp - 1)\r
-      {\r
-        hiddenIndex = tmp;\r
-      }\r
+        gg.setColor(Color.blue);\r
+        if(below)\r
+        {\r
+          gg.fillPolygon(new int[]\r
+                         {getWidth()- av.charHeight,\r
+                         getWidth()- av.charHeight,\r
+                         getWidth()},\r
+                         new int[]\r
+                         {\r
+                         (i - starty) * av.charHeight +yoffset,\r
+                         (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,\r
+                         (i - starty) * av.charHeight+yoffset\r
+          }, 3);\r
+        }\r
+        if(above)\r
+        {\r
+          gg.fillPolygon(new int[]\r
+                        {getWidth()- av.charHeight,\r
+                        getWidth()- av.charHeight,\r
+                        getWidth() },\r
+                        new int[]\r
+                        {\r
+                        (i - starty+1) * av.charHeight +yoffset,\r
+                        (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,\r
+                        (i - starty+1) * av.charHeight +yoffset\r
+         }, 3);\r
 \r
-      if (hiddenIndex != tmp)\r
-      {\r
-        hiddenIndex = tmp;\r
-      }\r
+        }\r
+    }\r
 \r
-      hiddenIndex++;\r
+    void setHiddenFont(int i)\r
+    {\r
+      Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+                             av.getFont().getSize());\r
+      Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
+                           av.getFont().getSize());\r
 \r
       if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
         gg.setFont(bold);\r

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index b3d7cda..29e338c 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -121,7 +121,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
             {\r
               public void actionPerformed(ActionEvent e)\r
               {\r
-                av.getColumnSelection().hideColumns(res, av);\r
+                av.hideColumns(res, res+1);\r
                 ap.repaint();\r
                 if(ap.overviewPanel != null)\r
                   ap.overviewPanel.updateOverviewImage();\r
@@ -401,20 +401,29 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
         {\r
           gg.setColor(Color.blue);\r
           int res;\r
-          for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)\r
+          if(av.getShowHiddenMarkers())\r
           {\r
-            res = av.getColumnSelection().findHiddenRegionPosition( i )-startx;\r
+            for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();\r
+                 i++)\r
+            {\r
+\r
+              res = av.getColumnSelection().findHiddenRegionPosition(i) -\r
+                  startx;\r
 \r
-            gg.fillPolygon(new int[] { res*av.charWidth - av.charHeight/4,\r
-                                         res*av.charWidth + av.charHeight/4,\r
-                                         res*av.charWidth },\r
-                                new int[]\r
-                                {\r
-                                    y-av.charHeight/2 , y-av.charHeight/2 ,\r
-                                    y + 8\r
-                                }, 3);\r
+              if(res < 0 || res > endx-scalestartx)\r
+                continue;\r
 \r
+              gg.fillPolygon(new int[]\r
+                             {res * av.charWidth - av.charHeight / 4,\r
+                             res * av.charWidth + av.charHeight / 4,\r
+                             res * av.charWidth},\r
+                             new int[]\r
+                             {\r
+                             y - av.charHeight / 2, y - av.charHeight / 2,\r
+                             y + 8\r
+              }, 3);\r
 \r
+            }\r
           }\r
 \r
           if (reveal != null && reveal[0] > startx && reveal[0] < endx)\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c4de7cd..8623872 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -477,6 +477,35 @@ public class SeqCanvas extends JComponent
                 drawNorthScale(g, startRes, endx, ypos);\r
             }\r
 \r
+            if (av.hasHiddenColumns && av.showHiddenMarkers)\r
+            {\r
+              g.setColor(Color.blue);\r
+              int res;\r
+              for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();\r
+                   i++)\r
+              {\r
+                res = av.getColumnSelection().findHiddenRegionPosition(i) -\r
+                    startRes;\r
+\r
+                if (res < 0 || res > endx - startRes)\r
+                  continue;\r
+\r
+                gg.fillPolygon(new int[]\r
+                               {res * av.charWidth - av.charHeight / 4,\r
+                               res * av.charWidth + av.charHeight / 4,\r
+                               res * av.charWidth},\r
+                               new int[]\r
+                               {\r
+                               ypos - (av.charHeight / 2),\r
+                               ypos - (av.charHeight / 2),\r
+                               ypos - (av.charHeight / 2) + 8\r
+                }, 3);\r
+\r
+              }\r
+            }\r
+\r
+\r
+\r
             // When printing we have an extra clipped region,\r
             // the Printable page which we need to account for here\r
             Shape clip = g.getClip();\r
@@ -568,15 +597,14 @@ public class SeqCanvas extends JComponent
 \r
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
 \r
-          g1.setColor(Color.blue);\r
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
-                      startSeq + offset,\r
-                      (blockEnd - blockStart + 1) * av.charWidth - 1,\r
-                      startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth,\r
-                      startSeq + offset,\r
-                      (blockEnd - blockStart + 1) * av.charWidth,\r
-                      startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
+          if(av.getShowHiddenMarkers())\r
+          {\r
+            g1.setColor(Color.blue);\r
+            g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+                        startSeq + offset,\r
+                        (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+                        startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
+          }\r
 \r
           g1.translate( -screenY * av.charWidth, 0);\r
           screenY += blockEnd - blockStart + 1;\r
@@ -588,6 +616,7 @@ public class SeqCanvas extends JComponent
           blockEnd = blockStart + (endRes - startRes) - screenY;\r
           g1.translate(screenY * av.charWidth, 0);\r
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
           g1.translate( -screenY * av.charWidth, 0);\r
         }\r
       }\r