X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=af10e1d180a37114726ace7c78888867c4f25d5c;hb=8b08ad675b71e43e127d7be3b65c6d2f9d9094db;hp=3cc691032961f9dce429c557ad1095bfc759cf7d;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java index 3cc6910..af10e1d 100755 --- a/src/jalview/datamodel/BinarySequence.java +++ b/src/jalview/datamodel/BinarySequence.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* 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 @@ -18,15 +18,8 @@ */ package jalview.datamodel; -import jalview.analysis.PCA; - -import jalview.io.*; - -import jalview.jbgui.*; - import jalview.schemes.*; -import java.awt.*; /** @@ -45,22 +38,9 @@ public class BinarySequence extends Sequence * * @param s DOCUMENT ME! */ - public BinarySequence(SequenceI s) - { - super(s.getName(), s.getSequence(), s.getStart(), s.getEnd()); - } - - /** - * Creates a new BinarySequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - */ - public BinarySequence(String name, String sequence, int start, int end) + public BinarySequence(String s) { - super(name, sequence, start, end); + super("", s, 0, s.length()); } /** @@ -84,9 +64,7 @@ public class BinarySequence extends Sequence try { - aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence() - .substring(i, - i + 1))).intValue(); + aanum = ResidueProperties.aaIndex[getSequence().charAt(i)]; } catch (NullPointerException e) { @@ -121,9 +99,7 @@ public class BinarySequence extends Sequence try { - aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence() - .substring(i, - i + 1))).intValue(); + aanum = ResidueProperties.aaIndex[getSequence().charAt(i)]; } catch (NullPointerException e) { @@ -175,13 +151,4 @@ public class BinarySequence extends Sequence return dbinary; } - /** - * DOCUMENT ME! - * - * @param rt DOCUMENT ME! - */ - public static void printMemory(Runtime rt) - { - System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log. - } }