From d406dae9bb29125d7a7017e4eb6e2e45ba47135b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 30 Nov 2005 15:36:19 +0000
Subject: [PATCH 1/1] REpaint after sequence col selected

---
 src/MCview/AppletPDBCanvas.java |    6 +++---
 src/MCview/AppletPDBViewer.java |    1 +
 src/MCview/PDBCanvas.java       |   16 ++++++++--------
 src/MCview/PDBfile.java         |    4 ++--
 4 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index bdef555..f0b7514 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -202,6 +202,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
           }
         }
       }
+      updateSeqColours();
+      redrawneeded = true;
+      repaint();
     }
 
 
@@ -967,9 +970,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       mainchain.isVisible = true;
       findCentre();
       setupBonds();
-      redrawneeded = true;
-      repaint();
-
     }
 
 }
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 3f4e42c..8598c8d 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -207,6 +207,7 @@ public class AppletPDBViewer extends Frame
         clearButtonGroup();
         pdbcanvas.bysequence = true;
         pdbcanvas.updateSeqColours();
+        pdbcanvas.repaint();
       }
 
       void clearButtonGroup()
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index f853106..70f959f 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -189,8 +189,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
         scale = findScale();
 
-
-        updateSeqColours();
         ToolTipManager.sharedInstance().registerComponent(this);
         ToolTipManager.sharedInstance().setInitialDelay(0);
         ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -215,6 +213,10 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           }
         }
       }
+
+      updateSeqColours();
+      redrawneeded = true;
+      repaint();
     }
 
 
@@ -430,7 +432,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       {
         for (int ii = 0; ii < pdb.chains.size(); ii++)
         {
-          colourBySequence( mainchain );
+          colourBySequence( (PDBChain) pdb.chains.elementAt(ii));
         }
       }
 
@@ -478,6 +480,9 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         tmp.startCol = Color.lightGray;
         tmp.endCol = Color.lightGray;
 
+        if(chain!=mainchain)
+          continue;
+
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
         {
@@ -513,8 +518,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void drawScene(Graphics g)
     {
-
-
         if (zbuffer)
         {
             Zsort.Zsort(visiblebonds);
@@ -543,7 +546,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
                     g.setColor(tmpBond.startCol.darker().darker());
                     drawLine(g, xstart, ystart, xmid, ymid);
-
                     g.setColor(tmpBond.endCol.darker().darker());
                     drawLine(g, xmid, ymid, xend, yend);
                 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
@@ -976,7 +978,5 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       mainchain.isVisible = true;
       findCentre();
       setupBonds();
-      redrawneeded = true;
-      repaint();
     }
 }
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 47aa5ac..b3e4e28 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -105,8 +105,8 @@ public class PDBfile extends jalview.io.FileParse {
                         Atom tmpatom = new Atom(line);
 
                         //Jalview is only interested in CA bonds????
-                     //   if(!tmpatom.name.equals("CA"))
-                     //     continue;
+                        if(!tmpatom.name.equals("CA"))
+                          continue;
 
                         tmpchain = findChain(tmpatom.chain);
                         if ( tmpchain != null)
-- 
1.7.10.2