X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarCigar.java;fp=src%2Fjalview%2Fdatamodel%2FCigarCigar.java;h=bc89d2c5dc66f77382694de030e42ea85a9937c0;hb=59d682209891099d46b960509907c79e3fb276fe;hp=b77949836f1fac9322c0c869117176117adde0b7;hpb=d1b697c33b69a6dfe55df789eec5ac9881013681;p=jalview.git
diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index b779498..bc89d2c 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,61 +1,61 @@
-/*
- * 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
- *
- * 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 .
- */
-package jalview.datamodel;
-
-public class CigarCigar extends CigarSimple
-{
- SeqCigar refCigar;
-
- /**
- * Apply CIGAR operations to the result of another cigar
- *
- * @param cigar
- * Cigar
- */
- CigarCigar(SeqCigar cigar)
- {
- super();
- refCigar = cigar;
- }
-
- /**
- *
- * @return String formed by applying CIGAR operations to the reference object
- * @param GapChar
- * char
- * @todo Implement this jalview.datamodel.Cigar method
- */
- public String getSequenceString(char GapChar)
- {
- if (length == 0)
- {
- return "";
- }
- String refString = refCigar.getSequenceString(GapChar);
- if (refString != null)
- {
- return (length == 0) ? "" : (String) getSequenceAndDeletions(
- refString, GapChar)[0];
- }
- else
- {
- return null;
- }
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+package jalview.datamodel;
+
+public class CigarCigar extends CigarSimple
+{
+ SeqCigar refCigar;
+
+ /**
+ * Apply CIGAR operations to the result of another cigar
+ *
+ * @param cigar
+ * Cigar
+ */
+ CigarCigar(SeqCigar cigar)
+ {
+ super();
+ refCigar = cigar;
+ }
+
+ /**
+ *
+ * @return String formed by applying CIGAR operations to the reference object
+ * @param GapChar
+ * char
+ * @todo Implement this jalview.datamodel.Cigar method
+ */
+ public String getSequenceString(char GapChar)
+ {
+ if (length == 0)
+ {
+ return "";
+ }
+ String refString = refCigar.getSequenceString(GapChar);
+ if (refString != null)
+ {
+ return (length == 0) ? "" : (String) getSequenceAndDeletions(
+ refString, GapChar)[0];
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+}