treeFile = treeFile

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index c89d489..5265bc2 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,52 +1,58 @@
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
 package MCview;\r
-import java.util.*;\r
+\r
 import java.awt.*;\r
 \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
+    float x;\r
+    float y;\r
+    float z;\r
+    int number;\r
+    String name;\r
+    String resName;\r
+    int resNumber;\r
+    int type;\r
+    Color color = Color.lightGray;\r
+    String chain;\r
+    int alignmentMapping=-1;\r
+\r
+    public boolean isSelected = false;\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
+    public Atom(String str)\r
+    {\r
+        name =  str.substring(12,15).trim();\r
 \r
-  }\r
+        resName = str.substring(17,20);\r
 \r
-  public void setColor(Color col) {\r
-    this.color = col;\r
-  }\r
+        chain = str.substring(21,22);\r
+\r
+        resNumber = Integer.parseInt(str.substring(22,26).trim());\r
+\r
+        this.x = (float) (new Float(str.substring(30,38).trim()).floatValue());\r
+        this.y = (float) (new Float(str.substring(38,46).trim()).floatValue());\r
+        this.z = (float) (new Float(str.substring(47,55).trim()).floatValue());\r
+\r
+    }\r
 \r
+  //  public void setColor(Color col) {\r
+  //      this.color = col;\r
+  //  }\r
 }\r