X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=910c86df2bdb7dbc56363767d0ad42b116f3dd18;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=293528d13c186a1ef6db43720f0e8b615e0d4be1;hpb=1ad6a9b44ff7828a2a001ad1520b0ee652a466e2;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 293528d..910c86d 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
- *
+ *
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
@@ -54,9 +55,9 @@ public class Sequence implements SequenceI
* to the residues of this sequence
*/
Vector annotation;
-
+
/**
- * The index of the sequence in a MSA
+ * The index of the sequence in a MSA
*/
int index = -1;
@@ -122,7 +123,8 @@ public class Sequence implements SequenceI
void checkValidRange()
{
- // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
+ // Note: JAL-774 :
+ // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
{
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
@@ -137,7 +139,8 @@ public class Sequence implements SequenceI
endRes += start - 1;
}
- if (end _annot = annotation;
+ annotation = null;
+ for (AlignmentAnnotation aa : _annot)
+ {
+ aa.sequenceRef = datasetSequence;
+ aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(aa);
+ }
+ }
}
return datasetSequence;
}
@@ -1181,16 +1197,24 @@ public class Sequence implements SequenceI
}
/**
- * @return The index (zero-based) on this sequence in the MSA.
- * It returns {@code -1} if this information is not available.
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
*/
- public int getIndex() { return index; }
-
+ public int getIndex()
+ {
+ return index;
+ }
+
/**
- * Defines the position of this sequence in the MSA.
- * Use the value {@code -1} if this information is undefined.
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
*
- * @param The position for this sequence. This value is zero-based (zero for this first sequence)
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
*/
- public void setIndex(int value) { index = value; }
+ public void setIndex(int value)
+ {
+ index = value;
+ }
}