merge from 2_4_Release branch

[jalview.git] / src / MCview / Atom.java

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index c89d489..e69e1ce 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,52 +1,89 @@
-package MCview;\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class Atom {\r
-  double x;\r
-  double y;\r
-  double z;\r
-  int number;\r
-  String name;\r
-  String resName;\r
-  int resNumber;\r
-  int type;\r
-  Color color;\r
-  String chain;\r
-\r
-  public Atom(StringTokenizer str) {\r
-    this.number  = (new Integer(str.nextToken())).intValue();\r
-    this.name    = str.nextToken();\r
-    this.resName = str.nextToken();\r
-\r
-    String tmpstr = new String();\r
-\r
-    try {\r
-      tmpstr = str.nextToken();\r
-\r
-      this.resNumber = (new Integer(tmpstr).intValue());\r
-      this.chain     = "A";\r
-      this.color     = Color.green;\r
-\r
-    } catch(NumberFormatException e) {\r
-      this.chain = tmpstr;\r
-\r
-      if (tmpstr.equals("A")) {\r
-        this.color = new Color((float)Math.random(),(float)Math.random(),(float)Math.random());\r
-      } else {\r
-        this.color = Color.red;\r
-      }\r
-      this.resNumber = (new Integer(str.nextToken()).intValue());\r
-    }\r
-\r
-    this.x = (double)(new Double(str.nextToken()).floatValue());\r
-    this.y = (double)(new Double(str.nextToken()).floatValue());\r
-    this.z = (double)(new Double(str.nextToken()).floatValue());\r
-\r
-  }\r
-\r
-  public void setColor(Color col) {\r
-    this.color = col;\r
-  }\r
-\r
-}\r
+/*
+ * 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;
+  // }
+}