X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fclade_analysis%2FResult.java;h=e11fcd5510b6b32c667097a3c9fe01f02a1400da;hb=aca4b7b8dd799b10748337065bd6b3d7c7530e76;hp=e7686e1729090d052f98bb4442f142b3eb159d76;hpb=8298cc0323b6f4d4a905f31512f0b3adcc76f925;p=jalview.git

diff --git a/forester/java/src/org/forester/clade_analysis/Result.java b/forester/java/src/org/forester/clade_analysis/Result.java
index e7686e1..e11fcd5 100644
--- a/forester/java/src/org/forester/clade_analysis/Result.java
+++ b/forester/java/src/org/forester/clade_analysis/Result.java
@@ -36,9 +36,9 @@ public final class Result {
     private final List<String> _warnings                              = new ArrayList<>();
     private int                _lec_ext_nodes                         = 0;
     private int                _p_ext_nodes                           = 0;
-    private String             _greatest_common_clade_confidence      = "";
-    private String             _greatest_common_clade_confidence_up   = "";
-    private String             _greatest_common_clade_confidence_down = "";
+    private String             _greatest_common_clade_subtree_confidence      = "";
+    private String             _greatest_common_clade_subtree_confidence_up   = "";
+    private String             _greatest_common_clade_subtree_confidence_down = "";
 
     void addWarning( final String warning ) {
         _warnings.add( warning );
@@ -56,16 +56,16 @@ public final class Result {
         _greatest_common_prefix_down = greatest_common_prefix_down;
     }
 
-    void setGreatestCommonCladeConfidence( final String greatest_common_clade_confidence ) {
-        _greatest_common_clade_confidence = greatest_common_clade_confidence;
+    void setGreatestCommonCladeSubtreeConfidence( final String greatest_common_clade_confidence ) {
+        _greatest_common_clade_subtree_confidence = greatest_common_clade_confidence;
     }
 
-    void setGreatestCommonCladeUpConfidence( final String greatest_common_clade_confidence_up ) {
-        _greatest_common_clade_confidence_up = greatest_common_clade_confidence_up;
+    void setGreatestCommonCladeUpSubtreeConfidence( final String greatest_common_clade_confidence_up ) {
+        _greatest_common_clade_subtree_confidence_up = greatest_common_clade_confidence_up;
     }
 
-    void setGreatestCommonCladeDownConfidence( final String greatest_common_clade_confidence_down ) {
-        _greatest_common_clade_confidence_down = greatest_common_clade_confidence_down;
+    void setGreatestCommonCladeDownSubtreeConfidence( final String greatest_common_clade_confidence_down ) {
+        _greatest_common_clade_subtree_confidence_down = greatest_common_clade_confidence_down;
     }
 
     public String getGreatestCommonPrefix() {
@@ -80,16 +80,16 @@ public final class Result {
         return _greatest_common_prefix_down;
     }
 
-    public String getGreatestCommonCladeConfidence() {
-        return _greatest_common_clade_confidence;
+    public String getGreatestCommonCladeSubtreeConfidence() {
+        return _greatest_common_clade_subtree_confidence;
     }
 
-    public String getGreatestCommonCladeUpConfidence() {
-        return _greatest_common_clade_confidence_up;
+    public String getGreatestCommonCladeUpSubtreeConfidence() {
+        return _greatest_common_clade_subtree_confidence_up;
     }
 
-    public String getGreatestCommonCladeDownConfidence() {
-        return _greatest_common_clade_confidence_down;
+    public String getGreatestCommonCladeDownSubtreeConfidence() {
+        return _greatest_common_clade_subtree_confidence_down;
     }
 
     public List<String> getWarnings() {