Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index ba4f705..ff38c08 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -30,6 +30,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
+import jalview.util.Format;
 
 import java.awt.Color;
 import java.util.List;
@@ -54,6 +55,8 @@ public class Conservation
 
   private static final int GAP_INDEX = -1;
 
+  private static final Format FORMAT_3DP = new Format("%2.5f");
+
   SequenceI[] sequences;
 
   int start;
@@ -273,7 +276,7 @@ public class Conservation
        * or not conserved (-1)
        * Using TreeMap means properties are displayed in alphabetical order
        */
-      SortedMap<String, Integer> resultHash = new TreeMap<String, Integer>();
+      SortedMap<String, Integer> resultHash = new TreeMap<>();
       SymbolCounts symbolCounts = values.getSymbolCounts();
       char[] symbols = symbolCounts.symbols;
       int[] counts = symbolCounts.values;
@@ -567,7 +570,7 @@ public class Conservation
    */
   private void percentIdentity(ScoreMatrix sm)
   {
-    seqNums = new Vector<int[]>();
+    seqNums = new Vector<>();
     int i = 0, iSize = sequences.length;
     // Do we need to calculate this again?
     for (i = 0; i < iSize; i++)
@@ -622,7 +625,7 @@ public class Conservation
   protected void findQuality(int startCol, int endCol,
           ScoreMatrix scoreMatrix)
   {
-    quality = new Vector<Double>();
+    quality = new Vector<>();
 
     double max = -Double.MAX_VALUE;
     float[][] scores = scoreMatrix.getMatrix();
@@ -695,7 +698,7 @@ public class Conservation
 
       max = Math.max(max, bigtot);
 
-      quality.addElement(new Double(bigtot));
+      quality.addElement(Double.valueOf(bigtot));
     }
 
     double newmax = -Double.MAX_VALUE;
@@ -707,7 +710,7 @@ public class Conservation
       tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
 
       // System.out.println(tmp+ " " + j);
-      quality.setElementAt(new Double(tmp), j);
+      quality.setElementAt(Double.valueOf(tmp), j);
 
       if (tmp > newmax)
       {
@@ -721,8 +724,8 @@ public class Conservation
 
   /**
    * Complete the given consensus and quuality annotation rows. Note: currently
-   * this method will enlarge the given annotation row if it is too small,
-   * otherwise will leave its length unchanged.
+   * this method will reallocate the given annotation row if it is different to
+   * the calculated width, otherwise will leave its length unchanged.
    * 
    * @param conservation
    *          conservation annotation row
@@ -736,30 +739,25 @@ public class Conservation
   public void completeAnnotations(AlignmentAnnotation conservation,
           AlignmentAnnotation quality2, int istart, int alWidth)
   {
-    char[] sequence = getConsSequence().getSequence();
-    float minR;
-    float minG;
-    float minB;
-    float maxR;
-    float maxG;
-    float maxB;
-    minR = 0.3f;
-    minG = 0.0f;
-    minB = 0f;
-    maxR = 1.0f - minR;
-    maxG = 0.9f - minG;
-    maxB = 0f - minB; // scalable range for colouring both Conservation and
-    // Quality
+    SequenceI cons = getConsSequence();
+
+    /*
+     * colour scale for Conservation and Quality;
+     */
+    float minR = 0.3f;
+    float minG = 0.0f;
+    float minB = 0f;
+    float maxR = 1.0f - minR;
+    float maxG = 0.9f - minG;
+    float maxB = 0f - minB;
 
     float min = 0f;
     float max = 11f;
     float qmin = 0f;
     float qmax = 0f;
 
-    char c;
-
     if (conservation != null && conservation.annotations != null
-            && conservation.annotations.length < alWidth)
+            && conservation.annotations.length != alWidth)
     {
       conservation.annotations = new Annotation[alWidth];
     }
@@ -768,7 +766,7 @@ public class Conservation
     {
       quality2.graphMax = (float) qualityMaximum;
       if (quality2.annotations != null
-              && quality2.annotations.length < alWidth)
+              && quality2.annotations.length != alWidth)
       {
         quality2.annotations = new Annotation[alWidth];
       }
@@ -780,7 +778,7 @@ public class Conservation
     {
       float value = 0;
 
-      c = sequence[i];
+      char c = cons.getCharAt(i);
 
       if (Character.isDigit(c))
       {
@@ -813,7 +811,8 @@ public class Conservation
         value = quality.elementAt(i).floatValue();
         float vprop = value - qmin;
         vprop /= qmax;
-        quality2.annotations[i] = new Annotation(" ", String.valueOf(value),
+        String description = FORMAT_3DP.form(value);
+        quality2.annotations[i] = new Annotation(" ", description,
                 ' ', value, new Color(minR + (maxR * vprop),
                         minG + (maxG * vprop), minB + (maxB * vprop)));
       }
@@ -866,8 +865,8 @@ public class Conservation
    */
   String getTooltip(int column)
   {
-    char[] sequence = getConsSequence().getSequence();
-    char val = column < sequence.length ? sequence[column] : '-';
+    SequenceI cons = getConsSequence();
+    char val = column < cons.getLength() ? cons.getCharAt(column) : '-';
     boolean hasConservation = val != '-' && val != '0';
     int consp = column - start;
     String tip = (hasConservation && consp > -1 && consp < consSymbs.length)