REpaint after sequence col selected

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index bdef555..f0b7514 100755 (executable)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -202,6 +202,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
           }\r
         }\r
       }\r
+      updateSeqColours();\r
+      redrawneeded = true;\r
+      repaint();\r
     }\r
 \r
 \r
@@ -967,9 +970,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       mainchain.isVisible = true;\r
       findCentre();\r
       setupBonds();\r
-      redrawneeded = true;\r
-      repaint();\r
-\r
     }\r
 \r
 }\r

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 3f4e42c..8598c8d 100755 (executable)
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -207,6 +207,7 @@ public class AppletPDBViewer extends Frame
         clearButtonGroup();\r
         pdbcanvas.bysequence = true;\r
         pdbcanvas.updateSeqColours();\r
+        pdbcanvas.repaint();\r
       }\r
 \r
       void clearButtonGroup()\r

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index f853106..70f959f 100755 (executable)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -189,8 +189,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 \r
         scale = findScale();\r
 \r
-\r
-        updateSeqColours();\r
         ToolTipManager.sharedInstance().registerComponent(this);\r
         ToolTipManager.sharedInstance().setInitialDelay(0);\r
         ToolTipManager.sharedInstance().setDismissDelay(10000);\r
@@ -215,6 +213,10 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           }\r
         }\r
       }\r
+\r
+      updateSeqColours();\r
+      redrawneeded = true;\r
+      repaint();\r
     }\r
 \r
 \r
@@ -430,7 +432,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       {\r
         for (int ii = 0; ii < pdb.chains.size(); ii++)\r
         {\r
-          colourBySequence( mainchain );\r
+          colourBySequence( (PDBChain) pdb.chains.elementAt(ii));\r
         }\r
       }\r
 \r
@@ -478,6 +480,9 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         tmp.startCol = Color.lightGray;\r
         tmp.endCol = Color.lightGray;\r
 \r
+        if(chain!=mainchain)\r
+          continue;\r
+\r
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))\r
         {\r
@@ -513,8 +518,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 \r
     public void drawScene(Graphics g)\r
     {\r
-\r
-\r
         if (zbuffer)\r
         {\r
             Zsort.Zsort(visiblebonds);\r
@@ -543,7 +546,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {\r
                     g.setColor(tmpBond.startCol.darker().darker());\r
                     drawLine(g, xstart, ystart, xmid, ymid);\r
-\r
                     g.setColor(tmpBond.endCol.darker().darker());\r
                     drawLine(g, xmid, ymid, xend, yend);\r
                 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {\r
@@ -976,7 +978,5 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       mainchain.isVisible = true;\r
       findCentre();\r
       setupBonds();\r
-      redrawneeded = true;\r
-      repaint();\r
     }\r
 }\r

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 47aa5ac..b3e4e28 100755 (executable)
--- 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);\r
 \r
                         //Jalview is only interested in CA bonds????\r
-                     //   if(!tmpatom.name.equals("CA"))\r
-                     //     continue;\r
+                        if(!tmpatom.name.equals("CA"))\r
+                          continue;\r
 \r
                         tmpchain = findChain(tmpatom.chain);\r
                         if ( tmpchain != null)\r