JAL-4392 Consensus secondary structure: Display Secondary structure consensus for...

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

diff --git a/src/jalview/datamodel/ProfileI.java b/src/jalview/datamodel/ProfileI.java
index 65a5c0d..511095e 100644 (file)
--- a/src/jalview/datamodel/ProfileI.java
+++ b/src/jalview/datamodel/ProfileI.java
@@ -29,6 +29,8 @@ public interface ProfileI
    * @param residueCounts
    */
   public abstract void setCounts(ResidueCount residueCounts);
+  public abstract void setSSCounts(SecondaryStructureCount secondaryStructureCount);
+  
 
   /**
    * Returns the percentage identity of the profile, i.e. the highest proportion
@@ -39,6 +41,8 @@ public interface ProfileI
    * @return
    */
   public abstract float getPercentageIdentity(boolean ignoreGaps);
+  
+  public abstract float getSSPercentageIdentity(boolean ignoreGaps);
 
   /**
    * Returns the full symbol counts for this profile
@@ -68,6 +72,7 @@ public interface ProfileI
    * @return
    */
   public abstract int getMaxCount();
+  public abstract int getMaxSSCount();
 
   /**
    * Returns the symbol (or concatenated symbols) which have the highest count
@@ -76,6 +81,7 @@ public interface ProfileI
    * @return
    */
   public abstract String getModalResidue();
+  public abstract String getModalSS();
 
   /**
    * Answers the number of non-gapped sequences in the profile
@@ -83,5 +89,6 @@ public interface ProfileI
    * @return
    */
   public abstract int getNonGapped();
+  SecondaryStructureCount getSSCounts();
 
 }
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