X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=b7c919782d34612c66cd1ebe14331ae12e433e17;hb=8c6e707d6d9b1b8ad6385eb7eeef0bc78cb46f6e;hp=f16c009d1e7a1c848a5a4ca14fdf140431e422a8;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f16c009..b7c9197 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,82 +1,235 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* 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.
-*
-* 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * 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.
+ *
+ * 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
+ */
 package jalview.datamodel;
 
-import jalview.jbgui.*;
-
 import java.awt.*;
 
-import java.util.Vector;
-
-
-public interface SequenceI {
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public interface SequenceI
+{
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
     public void setName(String name);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getName();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     */
     public void setStart(int start);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int getStart();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getDisplayId();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param end DOCUMENT ME!
+     */
     public void setEnd(int end);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int getEnd();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int getLength();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sequence DOCUMENT ME!
+     */
     public void setSequence(String sequence);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getSequence();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getSequence(int start, int end);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public char getCharAt(int i);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param desc DOCUMENT ME!
+     */
     public void setDescription(String desc);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getDescription();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pos DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int findIndex(int pos);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int findPosition(int i);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int[] gapMap();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
     public void deleteChars(int i, int j);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
     public void deleteCharAt(int i);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
     public void insertCharAt(int i, char c);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     * @param chop DOCUMENT ME!
+     */
     public void insertCharAt(int i, char c, boolean chop);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
     public void setColor(Color c);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public Color getColor();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public Vector getSequenceFeatures();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
     public void setSequenceFeatures(Vector v);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
     public void setPDBId(String id);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getPDBId();
 }