JAL-891; structure logo is adapted to two char's; Missing: calculate

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

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 8338c9d..b9c61c2 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -469,10 +469,15 @@ public class StructureFrequency
    * @return
    */
   public static int[] extractProfile(Hashtable hconsensus,
-                 boolean ignoreGapsInConsensusCalculation)
+                 boolean ignoreGapsInConsensusCalculation,
+                 int column)
   {
-         //System.out.println("StructureFrequency.extractProfile");
-         int[] rtnval = new int[11];
+          //TODO is there a more elegant way to acces the column number?
+          /*
+           * calculate the frequence of the 16 bp variations for this column
+           * 'somehow' transfer this via getProfile and let it correctly draw
+           */
+          int[] rtnval = new int[22];
          int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
          if (profile == null)
                  return null;
@@ -493,10 +498,15 @@ public class StructureFrequency
                  if (((char[]) ca[c])[0] != '-')
                  {
                          rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
+                         //System.out.println("rtnval-"+c+": "+((char[]) ca[c])[0]);
                          rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
                                          : 0]);
                  }
          }
+         for(int i=0; i<rtnval.length;i++){
+         //  System.out.print(rtnval[i]+",");
+         }
+         System.out.print("\n");
          return rtnval;
   }