Merge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index ba4f705..0af5d20 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -273,7 +273,7 @@ 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 +567,7 @@ 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 +622,7 @@ 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();
@@ -721,8 +721,8 @@ 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 +736,25 @@ 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 +763,7 @@ 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 +775,7 @@ public class Conservation
     {
       float value = 0;
 
-      c = sequence[i];
+      char c = cons.getCharAt(i);
 
       if (Character.isDigit(c))
       {
@@ -866,8 +861,8 @@ 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)