From 02b51eb84c597f458ac4a5a41a5a328e760fc5be Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 17 Jan 2007 14:28:17 +0000
Subject: [PATCH] made atom attributes public (rather than put in get/set
 pairs)

---
 src/MCview/Atom.java |  120 ++++++++++++++++++++++++++------------------------
 1 file changed, 62 insertions(+), 58 deletions(-)

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index f907dff..fb9395a 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,58 +1,62 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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 {
-    float x;
-    float y;
-    float z;
-    int number;
-    String name;
-    String resName;
-    int resNumber;
-    int type;
-    Color color = Color.lightGray;
-    String chain;
-    int alignmentMapping=-1;
-
-    public boolean isSelected = false;
-
-    public Atom(String str)
-    {
-        name =  str.substring(12,15).trim();
-
-        resName = str.substring(17,20);
-
-        chain = str.substring(21,22);
-
-        resNumber = Integer.parseInt(str.substring(22,26).trim());
-
-        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());
-
-    }
-
-  //  public void setColor(Color col) {
-  //      this.color = col;
-  //  }
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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 int type;
+    Color color = Color.lightGray;
+    public String chain;
+    int alignmentMapping=-1;
+
+    public boolean isSelected = false;
+
+    public Atom(String str)
+    {
+        name =  str.substring(12,15).trim();
+
+        resName = str.substring(17,20);
+
+        chain = str.substring(21,22);
+
+        resNumber = Integer.parseInt(str.substring(22,26).trim());
+
+        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());
+
+    }
+    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;
+  //  }
+}
-- 
1.7.10.2