Sequence is char []

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

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index af10e1d..49e3543 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -49,7 +49,7 @@ public class BinarySequence extends Sequence
     public void encode()\r
     {\r
         // Set all matrix to 0\r
-        dbinary = new double[getSequence().length() * 21];\r
+        dbinary = new double[getSequence().length * 21];\r
 \r
         int nores = 21;\r
 \r
@@ -58,13 +58,13 @@ public class BinarySequence extends Sequence
             dbinary[i] = 0.0;\r
         }\r
 \r
-        for (int i = 0; i < getSequence().length(); i++)\r
+        for (int i = 0; i < getSequence().length; i++)\r
         {\r
             int aanum = 20;\r
 \r
             try\r
             {\r
-                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];\r
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];\r
             }\r
             catch (NullPointerException e)\r
             {\r
@@ -86,20 +86,20 @@ public class BinarySequence extends Sequence
     public void blosumEncode()\r
     {\r
         // Set all matrix to 0\r
-        dbinary = new double[getSequence().length() * 21];\r
+        dbinary = new double[getSequence().length * 21];\r
 \r
         int nores = 21;\r
 \r
         //for (int i = 0; i < dbinary.length; i++) {\r
         //  dbinary[i] = 0.0;\r
         //}\r
-        for (int i = 0; i < getSequence().length(); i++)\r
+        for (int i = 0; i < getSequence().length; i++)\r
         {\r
             int aanum = 20;\r
 \r
             try\r
             {\r
-                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];\r
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];\r
             }\r
             catch (NullPointerException e)\r
             {\r