PDB structure viewer updated

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0aaf040..51c4f01 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -20,13 +20,11 @@ package MCview;
 \r
 import java.awt.*;\r
 \r
-import java.util.*;\r
-\r
 \r
 public class Atom {\r
-    double x;\r
-    double y;\r
-    double z;\r
+    float x;\r
+    float y;\r
+    float z;\r
     int number;\r
     String name;\r
     String resName;\r
@@ -34,36 +32,24 @@ public class Atom {
     int type;\r
     Color color;\r
     String chain;\r
+    int alignmentMapping=-1;\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
+    public boolean isSelected = false;\r
 \r
-        String tmpstr = new String();\r
+    public Atom(String str)\r
+    {\r
+        name =  str.substring(12,15).trim();\r
 \r
-        try {\r
-            tmpstr = str.nextToken();\r
+        resName = str.substring(17,20);\r
 \r
-            this.resNumber = (new Integer(tmpstr).intValue());\r
-            this.chain = "A";\r
-            this.color = Color.green;\r
-        } catch (NumberFormatException e) {\r
-            this.chain = tmpstr;\r
+        chain = str.substring(21,22);\r
 \r
-            if (tmpstr.equals("A")) {\r
-                this.color = new Color((float) Math.random(),\r
-                        (float) Math.random(), (float) Math.random());\r
-            } else {\r
-                this.color = Color.red;\r
-            }\r
+        resNumber = Integer.parseInt(str.substring(22,26).trim());\r
 \r
-            this.resNumber = (new Integer(str.nextToken()).intValue());\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
-        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
     public void setColor(Color col) {\r