Jalview 2.6 source licence

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 7670452..13f928c 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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.
  * 
- * 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 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -62,14 +61,14 @@ public class Sequence implements SequenceI
    * Creates a new Sequence object.
    * 
    * @param name
-   *                display name string
+   *          display name string
    * @param sequence
-   *                string to form a possibly gapped sequence out of
+   *          string to form a possibly gapped sequence out of
    * @param start
-   *                first position of non-gap residue in the sequence
+   *          first position of non-gap residue in the sequence
    * @param end
-   *                last position of ungapped residues (nearly always only used
-   *                for display purposes)
+   *          last position of ungapped residues (nearly always only used for
+   *          display purposes)
    */
   public Sequence(String name, String sequence, int start, int end)
   {
@@ -141,9 +140,9 @@ public class Sequence implements SequenceI
    * Creates a new Sequence object.
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param sequence
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Sequence(String name, String sequence)
   {
@@ -156,7 +155,7 @@ public class Sequence implements SequenceI
    * reference.
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Sequence(SequenceI seq)
   {
@@ -169,9 +168,9 @@ public class Sequence implements SequenceI
    * annotation that is present in the given annotation array.
    * 
    * @param seq
-   *                the sequence to be copied
+   *          the sequence to be copied
    * @param alAnnotation
-   *                an array of annotation including some associated with seq
+   *          an array of annotation including some associated with seq
    */
   public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
   {
@@ -235,7 +234,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param v
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -331,7 +330,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param id
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setPDBId(Vector id)
   {
@@ -368,7 +367,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setName(String name)
   {
@@ -390,7 +389,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setStart(int start)
   {
@@ -411,7 +410,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setEnd(int end)
   {
@@ -442,7 +441,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setSequence(String seq)
   {
@@ -497,9 +496,9 @@ public class Sequence implements SequenceI
    * seqeunce
    * 
    * @param start
-   *                int
+   *          int
    * @param end
-   *                int
+   *          int
    * @return SequenceI
    */
   public SequenceI getSubSequence(int start, int end)
@@ -533,7 +532,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -553,7 +552,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDescription(String desc)
   {
@@ -574,7 +573,7 @@ public class Sequence implements SequenceI
    * Return the alignment position for a sequence position
    * 
    * @param pos
-   *                lying from start to end
+   *          lying from start to end
    * 
    * @return aligned position of residue pos
    */
@@ -608,7 +607,7 @@ public class Sequence implements SequenceI
    * Returns the sequence position for an alignment position
    * 
    * @param i
-   *                column index in alignment (from 1)
+   *          column index in alignment (from 1)
    * 
    * @return residue number for residue (left of and) nearest ith column
    */
@@ -765,11 +764,11 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param chop
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void insertCharAt(int i, int length, char c)
   {
@@ -991,8 +990,9 @@ public class Sequence implements SequenceI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
-   *      annotations)
+   * @see
+   * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+   * annotations)
    */
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
   {
@@ -1103,8 +1103,9 @@ public class Sequence implements SequenceI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
-   *      jalview.datamodel.Mapping)
+   * @see
+   * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
+   * jalview.datamodel.Mapping)
    */
   public void transferAnnotation(SequenceI entry, Mapping mp)
   {