JAL-1632 JAL-2416 load score matrices from file, as float[][]

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 7b9da46..8f7e57b 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -33,6 +33,7 @@ import java.awt.Color;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -243,7 +244,7 @@ public class Conservation
        * or not conserved (-1)
        * Using TreeMap means properties are displayed in alphabetical order
        */
-      Map<String, Integer> resultHash = new TreeMap<String, Integer>();
+      SortedMap<String, Integer> resultHash = new TreeMap<String, Integer>();
       SymbolCounts symbolCounts = values.getSymbolCounts();
       char[] symbols = symbolCounts.symbols;
       int[] counts = symbolCounts.values;
@@ -518,7 +519,7 @@ public class Conservation
    * 
    * @return Conservation sequence
    */
-  public Sequence getConsSequence()
+  public SequenceI getConsSequence()
   {
     return consSequence;
   }
@@ -601,7 +602,7 @@ public class Conservation
     quality = new Vector<Double>();
 
     double max = -10000;
-    int[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
+    float[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
 
     // Loop over columns // JBPNote Profiling info
     // long ts = System.currentTimeMillis();