retrieve all sequences matching a particular name (JAL-872)

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0a3bd39..25a3dc6 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -45,6 +45,9 @@ 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;