JAL-891; Tooltips for Structure logos implemented;

Change-Id: I8601aa5b9b9c50e9c1a7b8f6f39dd6f6e358cf6a

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 7b97a8d..42e8847 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -46,12 +46,15 @@ public class StructureFrequency
 
   public static final String PAIRPROFILE = "B";
 
-/**
- * Returns the 3' position of a base pair
- * @param pairs Secondary structure annotation
- * @param indice 5' position of a base pair
- * @return 3' position of a base pair
- */
+  /**
+   * Returns the 3' position of a base pair
+   * 
+   * @param pairs
+   *          Secondary structure annotation
+   * @param indice
+   *          5' position of a base pair
+   * @return 3' position of a base pair
+   */
   public static int findPair(SequenceFeature[] pairs, int indice)
   {
     for (int i = 0; i < pairs.length; i++)
@@ -96,9 +99,12 @@ public class StructureFrequency
       values = new int[255];
       pairs = new int[255][255];
       bpEnd = -1;
-      if(i<struc.length){
+      if (i < struc.length)
+      {
         s = struc[i];
-      }else{
+      }
+      else
+      {
         s = '-';
       }
       if (s == '.' || s == ' ')
@@ -178,13 +184,13 @@ public class StructureFrequency
         result[i] = residueHash;
       }
       if (bpEnd > 0)
-      {     
-        values[')']=values['('];
-        values['(']=0;
-        
+      {
+        values[')'] = values['('];
+        values['('] = 0;
+
         residueHash = new Hashtable();
         maxResidue = ")";
-        
+
         if (profile)
         {
           residueHash.put(PROFILE, new int[][]
@@ -193,14 +199,13 @@ public class StructureFrequency
 
           residueHash.put(PAIRPROFILE, pairs);
         }
-        
+
         residueHash.put(MAXCOUNT, new Integer(count));
         residueHash.put(MAXRESIDUE, maxResidue);
 
         percentage = ((float) count * 100) / (float) jSize;
         residueHash.put(PID_GAPS, new Float(percentage));
 
-        
         result[bpEnd] = residueHash;
       }
     }
@@ -294,17 +299,6 @@ public class StructureFrequency
           boolean ignoreGapsInConsensusCalculation,
           boolean includeAllConsSymbols)
   {
-    completeConsensus(consensus, hconsensus, iStart, width,
-            ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
-    // char[]
-    // { 'A', 'C', 'G', 'T', 'U' });
-  }
-
-  public static void completeConsensus(AlignmentAnnotation consensus,
-          Hashtable[] hconsensus, int iStart, int width,
-          boolean ignoreGapsInConsensusCalculation,
-          boolean includeAllConsSymbols, char[] alphabet)
-  {
     float tval, value;
     if (consensus == null || consensus.annotations == null
             || consensus.annotations.length < width)
@@ -345,51 +339,53 @@ public class StructureFrequency
       }
       int[][] profile = (int[][]) hconsensus[i]
               .get(StructureFrequency.PROFILE);
-      if (profile != null && includeAllConsSymbols) // Just responsible for the
+      int[][] pairs = (int[][]) hconsensus[i]
+              .get(StructureFrequency.PAIRPROFILE);
+
+      if (pairs != null && includeAllConsSymbols) // Just responsible for the
       // tooltip
-      //TODO Update tooltips for Structure row
+      // TODO Update tooltips for Structure row
       {
         mouseOver = "";
-        if (alphabet != null)
+
+        /* 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 +=
+         * ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; } }
+         * else {
+         */
+        Object[] ca = new Object[625];
+        float[] vl = new float[625];
+        int x = 0;
+        for (int c = 65; c < 90; c++)
         {
-          for (int c = 0; c < alphabet.length; c++)
+          for (int d = 65; d < 90; d++)
           {
-            tval = ((float) profile[0][alphabet[c]])
-                    * 100f
-                    / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
-                            : 0];
-            mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
-                    + ((int) tval) + "%";
+            ca[x] = new int[]
+            { c, d };
+            vl[x] = (float) pairs[c][d];
+            x++;
           }
         }
-        else
+        jalview.util.QuickSort.sort(vl, ca);
+        int p = 0;
+
+        for (int c = 624; c > 0; c--)
         {
-          Object[] ca = new Object[profile[0].length];
-          float[] vl = new float[profile[0].length];
-          for (int c = 0; c < ca.length; c++)
-          {
-            ca[c] = new char[]
-            { (char) c };
-            vl[c] = (float) profile[0][c];
-          }
-          ;
-          jalview.util.QuickSort.sort(vl, ca);
-          for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+          if (vl[c] > 0)
           {
-            if (((char[]) ca[c])[0] != '-')
-            {
-              tval = ((float) profile[0][((char[]) ca[c])[0]])
-                      * 100f
-                      / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
-                              : 0];
-              mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
-                      + " " + ((int) tval) + "%";
-              p++;
+            tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+                    : 0]);
+            mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
+                    + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
+            p++;
 
-            }
           }
-
         }
+
+        // }
       }
       else
       {
@@ -407,13 +403,8 @@ public class StructureFrequency
    * @return profile of the given column
    */
   public static int[] extractProfile(Hashtable hconsensus,
-          boolean ignoreGapsInConsensusCalculation, int column)
+          boolean ignoreGapsInConsensusCalculation)
   {
-    // 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[51]; // 2*(5*5)+1
     int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
     int[][] pairs = (int[][]) hconsensus
@@ -421,33 +412,35 @@ public class StructureFrequency
 
     if (profile == null)
       return null;
-    
+
+    // TODO fix the object length, also do it in completeConsensus
     Object[] ca = new Object[625];
     float[] vl = new float[625];
-    int x=0;
+    int x = 0;
     for (int c = 65; c < 90; c++)
     {
-      for(int d = 65; d< 90; d++)
+      for (int d = 65; d < 90; d++)
       {
-      ca[x] = new int[]{ c, d};
-      vl[x] = (float) pairs[c][d];
-      x++;
+        ca[x] = new int[]
+        { c, d };
+        vl[x] = (float) pairs[c][d];
+        x++;
       }
     }
     jalview.util.QuickSort.sort(vl, ca);
-    
+
     rtnval[0] = 1;
-    for (int c=624; c>0; c--)
+    for (int c = 624; c > 0; c--)
     {
-      if (vl[c]>0)
+      if (vl[c] > 0)
       {
         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
                 : 0]);
-       }
+      }
     }
-    
+
     return rtnval;
   }
 

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 85b9465..9f0be75 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1669,7 +1669,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           //TODO check what happens for group selections
           return StructureFrequency.extractProfile(
                   aa.groupRef.consensusData[column], aa.groupRef
-                          .getIgnoreGapsConsensus(),column);
+                          .getIgnoreGapsConsensus());
         }
         // TODO extend annotation row to enable dynamic and static profile data
         // to
@@ -1678,10 +1678,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 && av.isShowSequenceLogo())
         {
           return StructureFrequency.extractProfile(av.hStrucConsensus[column],
-                  av.getIgnoreGapsConsensus(),column);
+                  av.getIgnoreGapsConsensus());
         }
       }
-
     }
     return null;
   }