X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=68a7c21e53bf0244449e1096b4a4a33466031ecb;hb=d2749ce7a8dba3edbb210e82ec9a7e0c6e28cecf;hp=0a3bd3988ed0fdb55b89d5ba64957cfc404d9452;hpb=9bfd2651e3fd3dbadf67f5831f56fb86b4626a46;p=jalview.git
diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0a3bd39..68a7c21 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,23 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
{
@@ -45,13 +50,20 @@ public class Atom
public String chain;
+ /**
+ * this is a temporary value - designed to store the position in sequence that
+ * this atom corresponds to after aligning the chain to a SequenceI object. Do
+ * not rely on its value being correct when visualizing sequence colourings on
+ * the structure - use the StructureSelectionManager's mapping instead.
+ */
public int alignmentMapping = -1;
public int atomIndex;
public float occupancy = 0;
-
+
public float tfactor = 0;
+
// need these if we ever want to export Atom data
// public boolean tfacset=true,occset=true;
public boolean isSelected = false;
@@ -63,30 +75,37 @@ 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);
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();
- } else {
+ if (tm.length() > 0)
+ {
+ occupancy = (new Float(tm)).floatValue();
+ }
+ else
+ {
occupancy = 1f; // default occupancy
// see note above: occset=false;
}
tm = str.substring(60, 66).trim();
- if (tm.length()>0)
+ if (tm.length() > 0)
+ {
+ tfactor = (new Float(tm).floatValue());
+ }
+ else
{
- tfactor = (float) (new Float(tm).floatValue());
- } else {
tfactor = 1f;
- //see note above: tfacset=false;
+ // see note above: tfacset=false;
}
}
@@ -96,7 +115,4 @@ public class Atom
this.y = y;
this.z = z;
}
- // public void setColor(Color col) {
- // this.color = col;
- // }
}