X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=ea49f6809ded43338c41cfb22260c4757f3d63b6;hb=b8b5c2410e8814caf24d216545f2266c8854f963;hp=f16c009d1e7a1c848a5a4ca14fdf140431e422a8;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f16c009..ea49f68 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,82 +1,261 @@
 /*
-* 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;
+import java.util.*;
 
 
-public interface SequenceI {
+/**
+ * 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();
 
-    public String getDisplayId();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDisplayId(boolean jvsuffix);
 
+    /**
+     * 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);
 
-    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();
 
-    public Vector getSequenceFeatures();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceFeature[] getSequenceFeatures();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
+    public void setSequenceFeatures(SequenceFeature [] features);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
+    public void setPDBId(Vector ids);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getPDBId();
+
+    public void addPDBId(PDBEntry entry);
+
+    public String getVamsasId();
+
+    public void setVamsasId(String id);
+
+    public void setDBRef(Vector dbs);
+
+    public Vector getDBRef();
+
+    public void addDBRef(DBRefEntry entry);
+
+    public void addSequenceFeature(SequenceFeature sf);
+
+    public void setDatasetSequence(SequenceI seq);
+
+    public SequenceI getDatasetSequence();
+
+    public AlignmentAnnotation [] getAnnotation();
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+
+    public SequenceGroup getHiddenSequences();
+
+    public void addHiddenSequence(SequenceI seq);
+
+    public void showHiddenSequence(SequenceI seq);
 
-    public void setSequenceFeatures(Vector v);
+    public void changeCase(boolean toUpper, int start, int end);
 
-    public void setPDBId(String id);
+    public void toggleCase(int start, int end);
 
-    public String getPDBId();
 }