X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=1eab77e906dacd7fd702e6fc8d3ca693da55d7c6;hb=661f9e271e4c0225773971848b7e310a20dbe967;hp=5f85916f8f1bc617f617b1770a1c56adf8041fdb;hpb=a48744baf419c7c2cbbc548e7e7eb5098fd93b56;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 5f85916..1eab77e 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 
@@ -27,7 +27,7 @@ import jalview.datamodel.*;
  * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
  * This class is used extensively in calculating alignment colourschemes that
  * depend on the amount of conservation in each alignment column.
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -49,7 +49,7 @@ public class StructureFrequency
 
   /**
    * Returns the 3' position of a base pair
-   * 
+   *
    * @param pairs
    *          Secondary structure annotation
    * @param indice
@@ -71,7 +71,7 @@ public class StructureFrequency
   /**
    * Method to calculate a 'base pair consensus row', very similar to nucleotide
    * consensus but takes into account a given structure
-   * 
+   *
    * @param sequences
    * @param start
    * @param end
@@ -175,7 +175,7 @@ public class StructureFrequency
       residueHash.put(MAXCOUNT, new Integer(count));
       residueHash.put(MAXRESIDUE, maxResidue);
 
-      percentage = ((float) count * 100) / (float) jSize;
+      percentage = ((float) count * 100) / jSize;
       residueHash.put(PID_GAPS, new Float(percentage));
 
       // percentage = ((float) count * 100) / (float) nongap;
@@ -204,7 +204,7 @@ public class StructureFrequency
         residueHash.put(MAXCOUNT, new Integer(count));
         residueHash.put(MAXRESIDUE, maxResidue);
 
-        percentage = ((float) count * 100) / (float) jSize;
+        percentage = ((float) count * 100) / jSize;
         residueHash.put(PID_GAPS, new Float(percentage));
 
         result[bpEnd] = residueHash;
@@ -214,7 +214,7 @@ public class StructureFrequency
 
   /**
    * Method to check if a base-pair is a canonical or a wobble bp
-   * 
+   *
    * @param up
    *          5' base
    * @param down
@@ -286,7 +286,7 @@ public class StructureFrequency
   /**
    * Compute all or part of the annotation row from the given consensus
    * hashtable
-   * 
+   *
    * @param consensus
    *          - pre-allocated annotation row
    * @param hconsensus
@@ -350,7 +350,7 @@ public class StructureFrequency
         mouseOver = "";
 
         /* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure?
-         * 
+         *
          * if (alphabet != null) { for (int c = 0; c < alphabet.length; c++) {
          * tval = ((float) profile[0][alphabet[c]]) 100f / (float)
          * profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver +=
@@ -366,7 +366,7 @@ public class StructureFrequency
           {
             ca[x] = new int[]
             { c, d };
-            vl[x] = (float) pairs[c][d];
+            vl[x] = pairs[c][d];
             x++;
           }
         }
@@ -377,7 +377,7 @@ public class StructureFrequency
         {
           if (vl[c] > 0)
           {
-            tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+            tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
                     : 0]);
             mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
                     + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
@@ -399,7 +399,7 @@ public class StructureFrequency
 
   /**
    * get the sorted base-pair profile for the given position of the consensus
-   * 
+   *
    * @param hconsensus
    * @return profile of the given column
    */
@@ -424,7 +424,7 @@ public class StructureFrequency
       {
         ca[x] = new int[]
         { c, d };
-        vl[x] = (float) pairs[c][d];
+        vl[x] = pairs[c][d];
         x++;
       }
     }
@@ -438,7 +438,7 @@ public class StructureFrequency
       {
         rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
         rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
-        rtnval[rtnval[0]] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+        rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
                 : 0]);
         rtnval[1]+=rtnval[rtnval[0]++];
       }