From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 30 Nov 2005 15:05:57 +0000 (+0000)
Subject: Remove deletebonds
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=56854ddc00e57ff6b5a4047d6f79e04a32771030;p=jalview.git

Remove deletebonds
---

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index a86a0dd..f853106 100755
--- 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;
         int seqstart = 0;
         int seqend = 0;
-        AlignSeq maxAlignseq = null;;
+        AlignSeq maxAlignseq = null;
 
         for (int i = 0; i < pdb.chains.size(); i++)
         {
@@ -142,9 +142,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         mainchain.isVisible = true;
         mainchain.makeExactMapping(maxAlignseq, sequence);
 
-      //  mainchain.sequence = sequence;
-
-      this.pdb = pdb;
+        this.pdb = pdb;
         this.prefsize = new Dimension(getWidth(), getHeight());
 
         //Initialize the matrices to identity
@@ -219,22 +217,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       }
     }
 
-   public void deleteBonds() {
-        scale = 0;
-        maxwidth = 0;
-
-        width[0] = 0;
-        width[1] = 0;
-        width[2] = 0;
-
-        centre[0] = 0;
-        centre[1] = 0;
-        centre[2] = 0;
-
-        for (int i = 0; i < pdb.chains.size(); i++) {
-            ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
-        }
-    }
 
     public void findWidth() {
         float[] max = new float[3];
@@ -448,7 +430,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       {
         for (int ii = 0; ii < pdb.chains.size(); ii++)
         {
-          colourBySequence( (PDBChain) pdb.chains.elementAt(ii) );
+          colourBySequence( mainchain );
         }
       }
 
@@ -828,19 +810,22 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
             if (chain.isVisible)
             {
+              Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-                for (int i = 0; i < chain.bonds.size(); i++)
-                {
-                    Bond tmpBond = (Bond) chain.bonds.elementAt(i);
+              for (int i = 0; i < bonds.size(); i++)
+              {
+                  Bond tmpBond = (Bond) bonds.elementAt(i);
 
-                    if (tmpBond.at1.isSelected)
-                    {
-                        labelAtom(g, tmpBond, 1);
-                    }
-                    else if (tmpBond.at2.isSelected)
-                    {
-                        labelAtom(g, tmpBond, 2);
-                    }
+                  if (tmpBond.at1.isSelected)
+                  {
+                      labelAtom(g, tmpBond, 1);
+                  }
+
+                  if (tmpBond.at2.isSelected)
+                  {
+
+                      labelAtom(g, tmpBond, 2);
+                  }
                 }
             }
         }
@@ -936,7 +921,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     }
 
    Bond highlightBond1, highlightBond2;
-   String alignMouseOver;
    public void highlightRes(int ii)
   {
 
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 276525b..1fade31 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -41,7 +41,6 @@ public class PDBChain {
     public int seqstart = 0;
     public int seqend = 0;
 
-    //public DrawableSequence ds;
     public PDBChain(String id) {
         this.id = id;
     }