X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=5265bc27943b406d29e5f733d9211338625da55b;hb=1148c09dfab7a0c4f3e4d148b8d6c8e64b5686c7;hp=b3a8fdb11955198d4ab41f1216dd0eabe0e13a58;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index b3a8fdb..5265bc2 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -16,56 +16,43 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
-import java.util.*;
-import java.awt.*;
 
-public class Atom {
-  double x;
-  double y;
-  double z;
-  int number;
-  String name;
-  String resName;
-  int resNumber;
-  int type;
-  Color color;
-  String chain;
+import java.awt.*;
 
-  public Atom(StringTokenizer str) {
-    this.number  = (new Integer(str.nextToken())).intValue();
-    this.name    = str.nextToken();
-    this.resName = str.nextToken();
 
-    String tmpstr = new String();
+public class Atom {
+    float x;
+    float y;
+    float z;
+    int number;
+    String name;
+    String resName;
+    int resNumber;
+    int type;
+    Color color = Color.lightGray;
+    String chain;
+    int alignmentMapping=-1;
 
-    try {
-      tmpstr = str.nextToken();
+    public boolean isSelected = false;
 
-      this.resNumber = (new Integer(tmpstr).intValue());
-      this.chain     = "A";
-      this.color     = Color.green;
+    public Atom(String str)
+    {
+        name =  str.substring(12,15).trim();
 
-    } catch(NumberFormatException e) {
-      this.chain = tmpstr;
+        resName = str.substring(17,20);
 
-      if (tmpstr.equals("A")) {
-        this.color = new Color((float)Math.random(),(float)Math.random(),(float)Math.random());
-      } else {
-        this.color = Color.red;
-      }
-      this.resNumber = (new Integer(str.nextToken()).intValue());
-    }
+        chain = str.substring(21,22);
 
-    this.x = (double)(new Double(str.nextToken()).floatValue());
-    this.y = (double)(new Double(str.nextToken()).floatValue());
-    this.z = (double)(new Double(str.nextToken()).floatValue());
+        resNumber = Integer.parseInt(str.substring(22,26).trim());
 
-  }
+        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());
 
-  public void setColor(Color col) {
-    this.color = col;
-  }
+    }
 
+  //  public void setColor(Color col) {
+  //      this.color = col;
+  //  }
 }