drawableSequence removed

[jalview.git] / src / jalview / analysis / Conservation.java

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 520036e..c5ddd0f 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -32,16 +32,14 @@ public class Conservation {
 \r
   String consString = "";\r
 \r
-  DrawableSequence consSequence;\r
+  Sequence consSequence;\r
   Hashtable        propHash;\r
   int              threshold;\r
-  Hashtable[]      freqs;\r
 \r
   String name = "";\r
 \r
-  public Conservation(String name,Hashtable[] freqs,Hashtable propHash, int threshold, Vector sequences, int start, int end) {\r
+  public Conservation(String name,Hashtable propHash, int threshold, Vector sequences, int start, int end) {\r
     this.name      = name;\r
-    this.freqs     = freqs;\r
     this.propHash  = propHash;\r
     this.threshold = threshold;\r
     this.sequences = sequences;\r
@@ -121,17 +119,19 @@ public class Conservation {
     }\r
   }\r
 \r
-  public int countGaps(int j) {\r
+  public int countGaps(int j)\r
+  {\r
     int count = 0;\r
 \r
-    for (int i = 0; i < sequences.size();i++) {\r
+    for (int i = 0; i < sequences.size();i++)\r
+    {\r
       if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())\r
       {  count++; continue;}\r
 \r
-      String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);\r
-      if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {\r
+      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);\r
+      if (jalview.util.Comparison.isGap((c)))\r
         count++;\r
-      }\r
+\r
     }\r
     return count;\r
   }\r
@@ -182,10 +182,10 @@ public class Conservation {
       }\r
     }\r
 \r
-    consSequence = new DrawableSequence(name,consString,start,end);\r
+    consSequence = new Sequence(name,consString,start,end);\r
   }\r
 \r
-  public jalview.gui.DrawableSequence getConsSequence() {\r
+  public Sequence getConsSequence() {\r
     return consSequence;\r
   }\r
 \r