X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=e69e1ce6d99d8fd4f0bf88a903234c10d237a483;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=c89d48922bb19464f35fa079c09405e997b25375;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index c89d489..e69e1ce 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,52 +1,89 @@
-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 (Version 2.4)
+ * Copyright (C) 2008 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;
+
+  public int alignmentMapping = -1;
+
+  public int atomIndex;
+
+  public float occupancy = 0;
+
+  public float tfactor = 0;
+
+  public boolean isSelected = false;
+
+  public Atom(String str)
+  {
+    atomIndex = Integer.parseInt(str.substring(6, 11).trim());
+
+    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());
+    occupancy = (float) (new Float(str.substring(54, 60).trim())
+            .floatValue());
+    tfactor = (float) (new Float(str.substring(60, 66).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;
+  // }
+}