X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=904e3070c626cf00a1689be96aad34da9cdfbb0d;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=5f402381c180ad48635107acc31b94292d490b32;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 5f40238..904e307 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,24 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.awt.*;
+import jalview.schemes.ResidueProperties;
+
+import java.awt.Color;
public class Atom
{
@@ -71,20 +75,22 @@ public class Atom
name = str.substring(12, 15).trim();
resName = str.substring(17, 20);
+ // JAL-1828 treat MSE Selenomethionine as MET (etc)
+ resName = ResidueProperties.getCanonicalAminoAcid(resName);
chain = str.substring(21, 22);
resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27);
+ resNumIns = str.substring(22, 27).trim();
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());
+ this.x = (new Float(str.substring(30, 38).trim()).floatValue());
+ this.y = (new Float(str.substring(38, 46).trim()).floatValue());
+ this.z = (new Float(str.substring(47, 55).trim()).floatValue());
// optional entries - see JAL-730
String tm = str.substring(54, 60).trim();
if (tm.length() > 0)
{
- occupancy = (float) (new Float(tm)).floatValue();
+ occupancy = (new Float(tm)).floatValue();
}
else
{
@@ -94,7 +100,7 @@ public class Atom
tm = str.substring(60, 66).trim();
if (tm.length() > 0)
{
- tfactor = (float) (new Float(tm).floatValue());
+ tfactor = (new Float(tm).floatValue());
}
else
{
@@ -103,13 +109,28 @@ public class Atom
}
}
+ @Override
+ public boolean equals(Object that)
+ {
+ if (this == that || that == null)
+ {
+ return true;
+ }
+ if (that instanceof Atom)
+ {
+ Atom other = (Atom) that;
+ return other.resName.equals(this.resName)
+ && other.resNumber == this.resNumber
+ && other.resNumIns.equals(this.resNumIns)
+ && other.chain.equals(this.chain);
+ }
+ return false;
+ }
+
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;
- // }
}