/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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
{
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 tfactor = 0;
+ // need these if we ever want to export Atom data
+ // public boolean tfacset=true,occset=true;
public boolean isSelected = false;
public Atom(String str)
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());
- occupancy = (float) (new Float(str.substring(54, 60).trim())
- .floatValue());
- tfactor = (float) (new Float(str.substring(60, 66).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 = (new Float(tm)).floatValue();
+ }
+ else
+ {
+ occupancy = 1f; // default occupancy
+ // see note above: occset=false;
+ }
+ tm = str.substring(60, 66).trim();
+ if (tm.length() > 0)
+ {
+ tfactor = (new Float(tm).floatValue());
+ }
+ else
+ {
+ tfactor = 1f;
+ // see note above: tfacset=false;
+ }
+ }
+
+ @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.y = y;
this.z = z;
}
- // public void setColor(Color col) {
- // this.color = col;
- // }
}