Load pdb file with applet

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index b3a8fdb..51c4f01 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -16,56 +16,43 @@
 * 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
-\r
 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
+import java.awt.*;\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
+public class Atom {\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;\r
+    String chain;\r
+    int alignmentMapping=-1;\r
 \r
-    try {\r
-      tmpstr = str.nextToken();\r
+    public boolean isSelected = false;\r
 \r
-      this.resNumber = (new Integer(tmpstr).intValue());\r
-      this.chain     = "A";\r
-      this.color     = Color.green;\r
+    public Atom(String str)\r
+    {\r
+        name =  str.substring(12,15).trim();\r
 \r
-    } catch(NumberFormatException e) {\r
-      this.chain = tmpstr;\r
+        resName = str.substring(17,20);\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
+        chain = str.substring(21,22);\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
+        resNumber = Integer.parseInt(str.substring(22,26).trim());\r
 \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
-  public void setColor(Color col) {\r
-    this.color = col;\r
-  }\r
+    }\r
 \r
+    public void setColor(Color col) {\r
+        this.color = col;\r
+    }\r
 }\r