Remove deletebonds

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index a86a0dd..f853106 100755 (executable)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -88,7 +88,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         int pdbend = 0;\r
         int seqstart = 0;\r
         int seqend = 0;\r
-        AlignSeq maxAlignseq = null;;\r
+        AlignSeq maxAlignseq = null;\r
 \r
         for (int i = 0; i < pdb.chains.size(); i++)\r
         {\r
@@ -142,9 +142,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         mainchain.isVisible = true;\r
         mainchain.makeExactMapping(maxAlignseq, sequence);\r
 \r
-      //  mainchain.sequence = sequence;\r
-\r
-      this.pdb = pdb;\r
+        this.pdb = pdb;\r
         this.prefsize = new Dimension(getWidth(), getHeight());\r
 \r
         //Initialize the matrices to identity\r
@@ -219,22 +217,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       }\r
     }\r
 \r
-   public void deleteBonds() {\r
-        scale = 0;\r
-        maxwidth = 0;\r
-\r
-        width[0] = 0;\r
-        width[1] = 0;\r
-        width[2] = 0;\r
-\r
-        centre[0] = 0;\r
-        centre[1] = 0;\r
-        centre[2] = 0;\r
-\r
-        for (int i = 0; i < pdb.chains.size(); i++) {\r
-            ((PDBChain) pdb.chains.elementAt(i)).bonds = null;\r
-        }\r
-    }\r
 \r
     public void findWidth() {\r
         float[] max = new float[3];\r
@@ -448,7 +430,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       {\r
         for (int ii = 0; ii < pdb.chains.size(); ii++)\r
         {\r
-          colourBySequence( (PDBChain) pdb.chains.elementAt(ii) );\r
+          colourBySequence( mainchain );\r
         }\r
       }\r
 \r
@@ -828,19 +810,22 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 \r
             if (chain.isVisible)\r
             {\r
+              Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
 \r
-                for (int i = 0; i < chain.bonds.size(); i++)\r
-                {\r
-                    Bond tmpBond = (Bond) chain.bonds.elementAt(i);\r
+              for (int i = 0; i < bonds.size(); i++)\r
+              {\r
+                  Bond tmpBond = (Bond) bonds.elementAt(i);\r
 \r
-                    if (tmpBond.at1.isSelected)\r
-                    {\r
-                        labelAtom(g, tmpBond, 1);\r
-                    }\r
-                    else if (tmpBond.at2.isSelected)\r
-                    {\r
-                        labelAtom(g, tmpBond, 2);\r
-                    }\r
+                  if (tmpBond.at1.isSelected)\r
+                  {\r
+                      labelAtom(g, tmpBond, 1);\r
+                  }\r
+\r
+                  if (tmpBond.at2.isSelected)\r
+                  {\r
+\r
+                      labelAtom(g, tmpBond, 2);\r
+                  }\r
                 }\r
             }\r
         }\r
@@ -936,7 +921,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     }\r
 \r
    Bond highlightBond1, highlightBond2;\r
-   String alignMouseOver;\r
    public void highlightRes(int ii)\r
   {\r
 \r

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 276525b..1fade31 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -41,7 +41,6 @@ public class PDBChain {
     public int seqstart = 0;\r
     public int seqend = 0;\r
 \r
-    //public DrawableSequence ds;\r
     public PDBChain(String id) {\r
         this.id = id;\r
     }\r