From 6ddf2d553aee329db44dd36b564211c3880563ec Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:29:10 +0000
Subject: [PATCH] Hidden Rows

---
 src/jalview/gui/IdCanvas.java |   45 +++++++++++++++++++++++++++++++++++++----
 1 file changed, 41 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c2500c2..214f218 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -239,6 +239,7 @@ public class IdCanvas extends JPanel
             {
                 for (int i = starty; i < av.alignment.getHeight(); i++)
                 {
+
                     SequenceI s = av.alignment.getSequenceAt(i);
                     gg.setFont(italic);
                     drawIdString(gg, s, i, 0, ypos);
@@ -256,13 +257,33 @@ public class IdCanvas extends JPanel
         else
         {
             //Now draw the id strings
+            int tmp, hiddenIndex = starty;
+            boolean markHidden = false;
             for (int i = starty; i < endy; i++)
             {
+              if (av.hasHiddenRows)
+              {
+                tmp = av.adjustForHiddenSeqs(i);
+                if(hiddenIndex != tmp)
+                {
+                    hiddenIndex = tmp;
+                    markHidden = true;
+                }
+                else
+                  markHidden = false;
+
+                hiddenIndex++;
+              }
+
+              if(av.hasHiddenRows && av.alignment.getSequenceAt(i).getHiddenSequences()!=null)
+              {
+                currentTextColor = Color.blue;
+              }
+              else
                 // Selected sequence colours
                 if ((searchResults != null) &&
                         searchResults.contains(av.alignment.getSequenceAt(i)))
                 {
-                    gg.setColor(Color.black);
                     currentColor = Color.black;
                     currentTextColor = Color.white;
                 }
@@ -282,7 +303,23 @@ public class IdCanvas extends JPanel
                 gg.setColor(currentColor);
 
                 gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
-                    av.charHeight);
+                            av.charHeight);
+
+                if (markHidden)
+                {
+                  gg.setColor(Color.blue);
+               //   gg.drawLine(0, (i-starty)*av.charHeight, getWidth(),(i-starty)*av.charHeight);
+                  gg.fillPolygon(new int[] { getWidth() - av.charHeight,
+                                         getWidth() - av.charHeight,
+                                         getWidth() },
+                                new int[]
+                                {
+                                    (i-starty)*av.charHeight -av.charHeight/4,
+                                    (i-starty)*av.charHeight +av.charHeight/4,
+                                    (i-starty)*av.charHeight
+                                }, 3);
+
+                }
 
                 gg.setColor(currentTextColor);
 
@@ -294,8 +331,8 @@ public class IdCanvas extends JPanel
             }
 
             // add a border
-            gg.setColor(Color.white);
-            gg.fillRect(getWidth() - 4, 0, 4, getHeight());
+         //   gg.setColor(Color.cyan);
+          //  gg.fillRect(getWidth() - 4, 0, 4, getHeight());
         }
     }
 
-- 
1.7.10.2