Clustal colours now work

[jalview.git] / src / jalview / schemes / Consensus.java

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 7b0dbbb..17cb789 100755 (executable)
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -18,8 +18,6 @@
 \r
 package jalview.schemes;\r
 \r
-import jalview.datamodel.*;\r
-import java.util.*;\r
 ////////////////////////////////////////////\r
 // This does nothing at all at the moment!!!!!!!!!!\r
 // AW 15th Dec 2004\r
@@ -28,25 +26,29 @@ public class Consensus {
 \r
   int[] mask;\r
   double threshold;\r
+   String maskstr;\r
 \r
-  public Consensus(String m, double threshold)\r
-  {\r
-    mask = setNums(m);\r
+  public Consensus(String mask, double threshold) {\r
+    // this.id = id;\r
+    //    this.mask = mask;\r
+        this.maskstr = mask;\r
+    setMask(mask);\r
     this.threshold = threshold;\r
   }\r
 \r
+  public void setMask(String s) {\r
+    this.mask = setNums(s);\r
+    //   for (int i=0; i < mask.length; i++) {\r
+    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
+    // }\r
+  }\r
 \r
-  public boolean isConserved(int[][] cons2,int col, int res,int size)\r
-  {\r
+  public boolean isConserved(int[][] cons2,int col ,int size) {\r
     int tot = 0;\r
-\r
-try{\r
-    for (int i=0; i < mask.length; i++)\r
+    for (int i = 0; i < mask.length; i++)\r
       tot += cons2[col][mask[i]];\r
-}catch(Exception ex)\r
-{ return true; }\r
 \r
-    if ((double)tot > threshold*size/100)\r
+    if ( (double) tot > threshold * size / 100)\r
       return true;\r
 \r
     return false;\r
@@ -60,7 +62,9 @@ try{
     {\r
       out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();\r
       i++;\r
+\r
     }\r
+\r
     return out;\r
   }\r
 \r