X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=e22b94ef5687016e7bdeae39b8b8e82691724c27;hb=41e1e412121ed83380bd33fcb9e3969dc055aa4c;hp=b3a8fdb11955198d4ab41f1216dd0eabe0e13a58;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index b3a8fdb..e22b94e 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,71 +1,72 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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.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) 2007 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;
+  //  }
+}