JAL-1306 calculate Quality also when Conservation not enabled

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 21d990c..01a14c9 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -24,11 +24,12 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 
 import java.awt.Color;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 /**
@@ -45,13 +46,14 @@ public class Conservation
 
   int end;
 
-  Vector seqNums; // vector of int vectors where first is sequence checksum
+  Vector<int[]> seqNums; // vector of int vectors where first is sequence
+                         // checksum
 
   int maxLength = 0; // used by quality calcs
 
   boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
 
-  Hashtable[] total;
+  Hashtable<String, Integer>[] total;
 
   boolean canonicaliseAa = true; // if true then conservation calculation will
 
@@ -60,16 +62,14 @@ public class Conservation
   // symbol
 
   /** Stores calculated quality values */
-  public Vector quality;
+  public Vector<Double> quality;
 
   /** Stores maximum and minimum values of quality values */
-  public Double[] qualityRange = new Double[2];
-
-  String consString = "";
+  private double[] qualityRange = new double[2];
 
   Sequence consSequence;
 
-  Hashtable propHash;
+  Map<String, Map<String, Integer>> propHash;
 
   int threshold;
 
@@ -151,7 +151,7 @@ public class Conservation
         seqNums.addElement(new int[sq.length() + 1]);
       }
 
-      if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
+      if (sq.hashCode() != seqNums.elementAt(i)[0])
       {
         int j;
         int len;
@@ -193,12 +193,9 @@ public class Conservation
    */
   public void calculate()
   {
-    Hashtable resultHash, ht;
     int thresh, j, jSize = sequences.length;
     int[] values; // Replaces residueHash
-    String type, res = null;
     char c;
-    Enumeration enumeration2;
 
     total = new Hashtable[maxLength];
 
@@ -214,8 +211,7 @@ public class Conservation
 
           if (canonicaliseAa)
           { // lookup the base aa code symbol
-            c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
-                    .getCharAt(i)];
+            c = (char) ResidueProperties.aaIndex[sequences[j].getCharAt(i)];
             if (c > 20)
             {
               c = '-';
@@ -223,7 +219,7 @@ public class Conservation
             else
             {
               // recover canonical aa symbol
-              c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
+              c = ResidueProperties.aa[c].charAt(0);
             }
           }
           else
@@ -249,21 +245,19 @@ public class Conservation
       thresh = (threshold * (jSize)) / 100;
 
       // loop over all the found residues
-      resultHash = new Hashtable();
+      Hashtable<String, Integer> resultHash = new Hashtable<String, Integer>();
       for (char v = '-'; v < 'Z'; v++)
       {
 
         if (values[v] > thresh)
         {
-          res = String.valueOf(v);
+          String res = String.valueOf(v);
 
           // Now loop over the properties
-          enumeration2 = propHash.keys();
-
-          while (enumeration2.hasMoreElements())
+          for (String type : propHash.keySet())
           {
-            type = (String) enumeration2.nextElement();
-            ht = (Hashtable) propHash.get(type);
+            Hashtable<String, Integer> ht = (Hashtable<String, Integer>) propHash
+                    .get(type);
 
             // Have we ticked this before?
             if (!resultHash.containsKey(type))
@@ -277,7 +271,7 @@ public class Conservation
                 resultHash.put(type, ht.get("-"));
               }
             }
-            else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
+            else if (!resultHash.get(type).equals(ht.get(res)))
             {
               resultHash.put(type, new Integer(-1));
             }
@@ -364,7 +358,7 @@ public class Conservation
    * Calculates the conservation sequence
    * 
    * @param consflag
-   *          if true, poitiveve conservation; false calculates negative
+   *          if true, positive conservation; false calculates negative
    *          conservation
    * @param percentageGaps
    *          commonly used value is 25
@@ -372,13 +366,6 @@ public class Conservation
   public void verdict(boolean consflag, float percentageGaps)
   {
     StringBuffer consString = new StringBuffer();
-    String type;
-    Integer result;
-    int[] gapcons;
-    int totGaps, count;
-    float pgaps;
-    Hashtable resultHash;
-    Enumeration enumeration;
 
     // NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
     // EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
@@ -390,26 +377,23 @@ public class Conservation
     consSymbs = new String[end - start + 1];
     for (int i = start; i <= end; i++)
     {
-      gapcons = countConsNGaps(i);
-      totGaps = gapcons[1];
-      pgaps = ((float) totGaps * 100) / sequences.length;
+      int[] gapcons = countConsNGaps(i);
+      int totGaps = gapcons[1];
+      float pgaps = ((float) totGaps * 100) / sequences.length;
       consSymbs[i - start] = new String();
 
       if (percentageGaps > pgaps)
       {
-        resultHash = total[i - start];
+        Hashtable<String, Integer> resultHash = total[i - start];
         // Now find the verdict
-        count = 0;
-        enumeration = resultHash.keys();
-
-        while (enumeration.hasMoreElements())
+        int count = 0;
+        for (String type : resultHash.keySet())
         {
-          type = (String) enumeration.nextElement();
-          result = (Integer) resultHash.get(type);
+          int result = resultHash.get(type).intValue();
           // Do we want to count +ve conservation or +ve and -ve cons.?
           if (consflag)
           {
-            if (result.intValue() == 1)
+            if (result == 1)
             {
               consSymbs[i - start] = type + " " + consSymbs[i - start];
               count++;
@@ -417,19 +401,16 @@ public class Conservation
           }
           else
           {
-            if (result.intValue() != -1)
+            if (result != -1)
             {
+              if (result == 0)
               {
-                if (result.intValue() == 0)
-                {
-                  consSymbs[i - start] = consSymbs[i - start] + " !" + type;
-                }
-                else
-                {
-                  consSymbs[i - start] = type + " " + consSymbs[i - start];
-                }
+                consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+              }
+              else
+              {
+                consSymbs[i - start] = type + " " + consSymbs[i - start];
               }
-
               count++;
             }
           }
@@ -474,7 +455,7 @@ public class Conservation
    */
   private void percentIdentity2()
   {
-    seqNums = new Vector();
+    seqNums = new Vector<int[]>();
     // calcSeqNum(s);
     int i = 0, iSize = sequences.length;
     // Do we need to calculate this again?
@@ -501,7 +482,7 @@ public class Conservation
 
       while (j < sequences.length)
       {
-        sqnum = (int[]) seqNums.elementAt(j);
+        sqnum = seqNums.elementAt(j);
 
         for (i = 1; i < sqnum.length; i++)
         {
@@ -531,17 +512,17 @@ public class Conservation
   /**
    * Calculates the quality of the set of sequences
    * 
-   * @param start
+   * @param startRes
    *          Start residue
-   * @param end
+   * @param endRes
    *          End residue
    */
-  public void findQuality(int start, int end)
+  public void findQuality(int startRes, int endRes)
   {
-    quality = new Vector();
+    quality = new Vector<Double>();
 
     double max = -10000;
-    int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+    int[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
 
     // Loop over columns // JBPNote Profiling info
     // long ts = System.currentTimeMillis();
@@ -556,10 +537,10 @@ public class Conservation
 
     for (l = 0; l < size; l++)
     {
-      lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+      lengths[l] = seqNums.elementAt(l).length - 1;
     }
 
-    for (j = start; j <= end; j++)
+    for (j = startRes; j <= endRes; j++)
     {
       bigtot = 0;
 
@@ -583,7 +564,7 @@ public class Conservation
       {
         tot = 0;
         xx = new double[24];
-        seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1]
+        seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1]
                 : 23; // Sequence, or gap at the end
 
         // This is a loop over r
@@ -617,9 +598,9 @@ public class Conservation
 
     double newmax = -10000;
 
-    for (j = start; j <= end; j++)
+    for (j = startRes; j <= endRes; j++)
     {
-      tmp = ((Double) quality.elementAt(j)).doubleValue();
+      tmp = quality.elementAt(j).doubleValue();
       tmp = ((max - tmp) * (size - cons2[j][23])) / size;
 
       // System.out.println(tmp+ " " + j);
@@ -632,12 +613,12 @@ public class Conservation
     }
 
     // System.out.println("Quality " + s);
-    qualityRange[0] = new Double(0);
-    qualityRange[1] = new Double(newmax);
+    qualityRange[0] = 0D;
+    qualityRange[1] = newmax;
   }
 
   /**
-   * complete the given consensus and quuality annotation rows. Note: currently
+   * 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.
    * 
@@ -675,7 +656,7 @@ public class Conservation
 
     char c;
 
-    if (conservation.annotations != null
+    if (conservation != null && conservation.annotations != null
             && conservation.annotations.length < alWidth)
     {
       conservation.annotations = new Annotation[alWidth];
@@ -683,14 +664,14 @@ public class Conservation
 
     if (quality2 != null)
     {
-      quality2.graphMax = qualityRange[1].floatValue();
+      quality2.graphMax = (float) qualityRange[1];
       if (quality2.annotations != null
               && quality2.annotations.length < alWidth)
       {
         quality2.annotations = new Annotation[alWidth];
       }
-      qmin = qualityRange[0].floatValue();
-      qmax = qualityRange[1].floatValue();
+      qmin = (float) qualityRange[0];
+      qmax = (float) qualityRange[1];
     }
 
     for (int i = istart; i < alWidth; i++)
@@ -712,20 +693,23 @@ public class Conservation
         value = 10;
       }
 
-      float vprop = value - min;
-      vprop /= max;
-      int consp = i - start;
-      String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
-              : "";
-      conservation.annotations[i] = new Annotation(String.valueOf(c),
-              conssym, ' ', value, new Color(minR + (maxR * vprop), minG
-                      + (maxG * vprop), minB + (maxB * vprop)));
+      if (conservation != null)
+      {
+        float vprop = value - min;
+        vprop /= max;
+        int consp = i - start;
+        String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+                : "";
+        conservation.annotations[i] = new Annotation(String.valueOf(c),
+                conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+                        + (maxG * vprop), minB + (maxB * vprop)));
+      }
 
       // Quality calc
       if (quality2 != null)
       {
-        value = ((Double) quality.elementAt(i)).floatValue();
-        vprop = value - qmin;
+        value = quality.elementAt(i).floatValue();
+        float vprop = value - qmin;
         vprop /= qmax;
         quality2.annotations[i] = new Annotation(" ",
                 String.valueOf(value), ' ', value, new Color(minR

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 47227d5..a746e1f 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -807,7 +807,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConservation(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (alignment.isNucleotide() || conservation == null
+    if (alignment.isNucleotide()
+            || (conservation == null && quality == null)
             || !autoCalculateConsensus)
     {
       return;

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index eff3fdc..bbad963 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -26,9 +26,13 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.Sequence;
@@ -55,8 +59,7 @@ public class AlignViewportTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] { "-props",
-        "test/jalview/testProps.jvprops" });
+    Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -297,4 +300,32 @@ public class AlignViewportTest
     assertTrue(ssmMappings.contains(acf2));
     assertFalse(ssmMappings.contains(acf3));
   }
+  
+  /**
+   * Test for JAL-1306 - conservation thread should run even when only Quality
+   * (and not Conservation) is enabled in Preferences
+   */
+  @Test(groups = { "Functional" })
+  public void testUpdateConservation_qualityOnly()
+  {
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.FALSE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    AlignmentAnnotation[] anns = af.viewport.getAlignment().getAlignmentAnnotation();
+    assertNotNull("No annotations found", anns);
+    assertEquals("More than one annotation found", 1, anns.length);
+    assertTrue("Annotation is not Quality",
+            anns[0].description.startsWith("Alignment Quality"));
+    Annotation[] annotations = anns[0].annotations;
+    assertNotNull("Quality annotations are null", annotations);
+    assertNotNull("Quality in column 1 is null", annotations[0]);
+    assertTrue("No quality value in column 1", annotations[0].value > 10f);
+  }
 }