X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=54e0dc85497de7a7a330edecef9c147d9482ac5d;hb=77c35fa912621cbadcf5ec74da4c6d45de6322e1;hp=c89d48922bb19464f35fa079c09405e997b25375;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index c89d489..54e0dc8 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,52 +1,65 @@
-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;
-
-  public Atom(StringTokenizer str) {
-    this.number  = (new Integer(str.nextToken())).intValue();
-    this.name    = str.nextToken();
-    this.resName = str.nextToken();
-
-    String tmpstr = new String();
-
-    try {
-      tmpstr = str.nextToken();
-
-      this.resNumber = (new Integer(tmpstr).intValue());
-      this.chain     = "A";
-      this.color     = Color.green;
-
-    } catch(NumberFormatException e) {
-      this.chain = tmpstr;
-
-      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());
-    }
-
-    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;
-  }
-
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* 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
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* 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.awt.*;
+
+
+public class Atom {
+    public float x;
+    public float y;
+    public float z;
+    public int number;
+    public String name;
+    public String resName;
+    public int resNumber;
+    public char insCode=' ';
+    public String resNumIns=null;
+    public int type;
+    Color color = Color.lightGray;
+    public String chain;
+    int alignmentMapping=-1;
+
+    public boolean isSelected = false;
+
+    public Atom(String str)
+    {
+        name =  str.substring(12,15).trim();
+
+        resName = str.substring(17,20);
+
+        chain = str.substring(21,22);
+
+        resNumber = Integer.parseInt(str.substring(22,26).trim());
+        resNumIns=str.substring(22,27);
+        insCode = str.substring(26,27).charAt(0);
+        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 Atom(float x,float y, float z) {
+      this.x = x;
+      this.y = y;
+      this.z = z;
+    }
+  //  public void setColor(Color col) {
+  //      this.color = col;
+  //  }
+}