X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=f907dff4c06b424ea47cde40f01e0d4b5255cc18;hb=99bd0585b045d25fa719ee007e3310d27e53ac88;hp=0aaf0409a13314e72fe59bf9391a25960e8ef538;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0aaf040..f907dff 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -20,53 +20,39 @@ package MCview;
 
 import java.awt.*;
 
-import java.util.*;
-
 
 public class Atom {
-    double x;
-    double y;
-    double z;
+    float x;
+    float y;
+    float z;
     int number;
     String name;
     String resName;
     int resNumber;
     int type;
-    Color color;
+    Color color = Color.lightGray;
     String chain;
+    int alignmentMapping=-1;
 
-    public Atom(StringTokenizer str) {
-        this.number = (new Integer(str.nextToken())).intValue();
-        this.name = str.nextToken();
-        this.resName = str.nextToken();
+    public boolean isSelected = false;
 
-        String tmpstr = new String();
+    public Atom(String str)
+    {
+        name =  str.substring(12,15).trim();
 
-        try {
-            tmpstr = str.nextToken();
+        resName = str.substring(17,20);
 
-            this.resNumber = (new Integer(tmpstr).intValue());
-            this.chain = "A";
-            this.color = Color.green;
-        } catch (NumberFormatException e) {
-            this.chain = tmpstr;
+        chain = str.substring(21,22);
 
-            if (tmpstr.equals("A")) {
-                this.color = new Color((float) Math.random(),
-                        (float) Math.random(), (float) Math.random());
-            } else {
-                this.color = Color.red;
-            }
+        resNumber = Integer.parseInt(str.substring(22,26).trim());
 
-            this.resNumber = (new Integer(str.nextToken()).intValue());
-        }
+        this.x = (float) (new Float(str.substring(30,38).trim()).floatValue());
+        this.y = (float) (new Float(str.substring(38,46).trim()).floatValue());
+        this.z = (float) (new Float(str.substring(47,55).trim()).floatValue());
 
-        this.x = (double) (new Double(str.nextToken()).floatValue());
-        this.y = (double) (new Double(str.nextToken()).floatValue());
-        this.z = (double) (new Double(str.nextToken()).floatValue());
     }
 
-    public void setColor(Color col) {
-        this.color = col;
-    }
+  //  public void setColor(Color col) {
+  //      this.color = col;
+  //  }
 }