Alignment quality with funky coloured histograms.

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index c5ddd0f..38047f8 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -27,14 +27,52 @@ public class Conservation {
   Vector sequences;\r
   int    start;\r
   int    end;\r
-\r
-  Vector total = new Vector();\r
-\r
-  String consString = "";\r
-\r
-  Sequence consSequence;\r
-  Hashtable        propHash;\r
-  int              threshold;\r
+  Vector seqNums; // vector of int vectors where first is sequence checksum\r
+  int maxLength=0; //  used by quality calcs\r
+  boolean seqNumsChanged = false; // updated after any change via calcSeqNum;\r
+  private void calcSeqNums() {\r
+    for (int i=0; i<sequences.size(); i++) {\r
+      calcSeqNum(i);\r
+    }\r
+  }\r
+  private void calcSeqNum(int i) {\r
+    String sq=null; // for dumb jbuilder not-inited exception warning\r
+    int[] sqnum = null;\r
+    if (i>-1 && i<sequences.size()) {\r
+      sq = ((SequenceI)sequences.elementAt(i)).getSequence();\r
+      if (seqNums.size()<=i) {\r
+        seqNums.add(new int[sq.length()+1]);\r
+      }\r
+      if (sq.hashCode()!=((int[])seqNums.elementAt(i))[0])\r
+       {\r
+         int j, len;\r
+         seqNumsChanged = true;\r
+         sq = ((SequenceI) sequences.elementAt(i)).getSequence();\r
+         len = sq.length();\r
+         if (maxLength < len)\r
+           maxLength = len;\r
+         sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length\r
+         sqnum[0] = sq.hashCode();\r
+         for (j = 1; j <= len; j++)\r
+         {\r
+           sqnum[j] = ( (Integer) jalview.schemes.ResidueProperties.aaHash.get(new\r
+               String(sq.substring(j - 1, j)))).intValue(); // yuk\r
+         }\r
+         seqNums.set(i, sqnum);\r
+       }\r
+     } else {\r
+       // JBPNote INFO level debug\r
+       System.out.println("calcSeqNum called with out of range sequence index for Alignment\n");\r
+     }\r
+   }\r
+   Vector total = new Vector();\r
+   public Vector quality;\r
+   public Double[] qualityRange = new Double[2];\r
+   String consString = "";\r
+\r
+   Sequence consSequence;\r
+   Hashtable        propHash;\r
+   int              threshold;\r
 \r
   String name = "";\r
 \r
@@ -45,6 +83,8 @@ public class Conservation {
     this.sequences = sequences;\r
     this.start     = start;\r
     this.end       = end;\r
+    seqNums = new Vector(sequences.size());\r
+    calcSeqNums();\r
   }\r
 \r
 \r
@@ -189,4 +229,139 @@ public class Conservation {
     return consSequence;\r
   }\r
 \r
+  // From Alignment.java in jalview118\r
+\r
+  public void findQuality() {\r
+    findQuality(0,maxLength-1);\r
+  }\r
+\r
+  int[][] cons2;\r
+\r
+  private void percentIdentity2() {\r
+    calcSeqNums(); // updates maxLength, too.\r
+    if (cons2==null || seqNumsChanged) {\r
+      cons2 = new int[maxLength][24];\r
+      // Initialize the array\r
+      for (int j=0;j<24;j++) {\r
+        for (int i=0; i < maxLength;i++) {\r
+          cons2[i][j] = 0;\r
+        }\r
+      }\r
+\r
+      int sqnum[];\r
+      int j = 0;\r
+      while(j < sequences.size()) {\r
+        sqnum=(int[])seqNums.elementAt(j);\r
+        for (int i = 1; i < sqnum.length; i++) {\r
+          cons2[i-1][sqnum[i]]++;\r
+        }\r
+        j++;\r
+      }\r
+\r
+      // unnecessary ?\r
+      /* for (int i=start; i <= end; i++) {\r
+           int max = -1000;\r
+    int maxi = -1;\r
+    int maxj = -1;\r
+\r
+    for (int j=0;j<24;j++) {\r
+        if (cons2[i][j] > max) {\r
+        max = cons2[i][j];\r
+        maxi = i;\r
+        maxj = j;\r
+      }\r
+\r
+    }\r
+  } */\r
+    }\r
+\r
+}\r
+\r
+\r
+public void findQuality(int start, int end) {\r
+    quality = new Vector();\r
+    double max = -10000;\r
+    String s = "";\r
+    int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();\r
+    //Loop over columns // JBPNote Profiling info\r
+    //    long ts = System.currentTimeMillis();\r
+    //long te = System.currentTimeMillis();\r
+    percentIdentity2();\r
+\r
+    int size = seqNums.size();\r
+    int[] lengths = new int[size];\r
+\r
+    for (int l = 0; l < size; l++)\r
+      lengths[l] = ((int[]) seqNums.get(l)).length;\r
+\r
+    for (int j=start; j <= end; j++) {\r
+      double bigtot = 0;\r
+\r
+      // First Xr = depends on column only\r
+      double x[] = new double[24];\r
+\r
+      for (int ii=0; ii < 24; ii++) {\r
+       x[ii] = 0;\r
+       try {\r
+         for (int i2=0; i2 < 24; i2++) {\r
+           x[ii]  += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;\r
+         }\r
+       } catch (Exception e) {\r
+         System.out.println("Exception : "  + e);\r
+       }\r
+       //System.out.println("X " + ii + " " + x[ii]);\r
+       x[ii] /= (size);\r
+       //System.out.println("X " + ii + " " + x[ii]);\r
+      }\r
+      // Now calculate D for each position and sum\r
+      for (int k=0; k < size; k++) {\r
+       double tot = 0;\r
+       double[] xx = new double[24];\r
+        int seqNum =\r
+            ((j+1)<lengths[size])\r
+            ? ((int[]) seqNums.get(k))[j+1]\r
+            : 23; // Sequence, or gap at the end\r
+\r
+        // This is a loop over r\r
+        for (int i=0; i < 23; i++) {\r
+          double sr = 0;\r
+          try {\r
+            sr = (double)BLOSUM62[i][seqNum]+4;\r
+          } catch (Exception e) {\r
+            System.out.println("Exception in sr " + e);\r
+          }\r
+          //Calculate X with another loop over residues\r
+\r
+          //  System.out.println("Xi " + i + " " + x[i] + " " + sr);\r
+          xx[i] = x[i] - sr;\r
+\r
+          tot += xx[i]*xx[i];\r
+        }\r
+        bigtot += Math.sqrt(tot);\r
+      }\r
+      // This is the quality for one column\r
+      if (max < bigtot) {max = bigtot;}\r
+      //      bigtot  = bigtot * (size-cons2[j][23])/size;\r
+\r
+      quality.addElement(new Double(bigtot));\r
+\r
+      s += "-";\r
+\r
+      // Need to normalize by gaps\r
+    }\r
+    double newmax=-10000;\r
+    for (int j=start; j <= end; j++) {\r
+     double tmp =  ((Double)quality.elementAt(j)).doubleValue();\r
+     tmp = (max - tmp)*(size-cons2[j][23])/size;\r
+     //     System.out.println(tmp+ " " + j);\r
+     quality.setElementAt(new Double(tmp),j);\r
+     if (tmp>newmax)\r
+       newmax = tmp;\r
+    }\r
+    //    System.out.println("Quality " + s);\r
+    qualityRange[0] = new Double(0);\r
+    qualityRange[1] = new Double(newmax);\r
+  }\r
+\r
+\r
 }\r

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 6179cfa..16ede50 100755 (executable)
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -18,4 +18,8 @@ public class Annotation
     secondaryStructure = ss;
     value = val;
   }
+  public Annotation(String displayChar, String desc, char ss, float val, Color colour) {
+    this(displayChar, desc, ss, val);
+    this.colour = colour;
+  }
 }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 9d63cde..43f6aff 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -83,29 +83,41 @@ public class AlignViewport
         alignment.getWidth());\r
     cons.calculate();\r
     cons.verdict(false, 100);\r
-\r
+    cons.findQuality();\r
     String sequence = cons.getConsSequence().getSequence();\r
+    float minR,minG,minB, maxR,maxG,maxB;\r
+    minR = 0.3f;\r
+    minG = 0f;\r
+    minB = 0f;\r
+    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring\r
+    float min = cons.qualityRange[0].floatValue();\r
+    float max = cons.qualityRange[1].floatValue();\r
+\r
     for (int i = 0; i < alignment.getWidth(); i++)\r
     {\r
-      int value = 0;\r
+      float value = 0;\r
       try\r
       {\r
-        value = Integer.parseInt(sequence.charAt(i) + "");\r
+        //value = Integer.parseInt(sequence.charAt(i) + "");\r
+        value = ((Double) cons.quality.get(i)).floatValue();\r
       }\r
       catch (Exception ex)\r
       {\r
         if (sequence.charAt(i) == '*') value = 10;\r
       }\r
-\r
+      float vprop = value-min;\r
+      vprop/=max;\r
       annotations[i] = new Annotation(sequence.charAt(i) + "",\r
-                                      "Conservation graph", ' ', value);\r
+                                      "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minB+maxB*vprop, minB+maxB*vprop));\r
     }\r
 \r
     if(conservation==null)\r
     {\r
       conservation = new AlignmentAnnotation("Conservation",\r
                                              "Conservation of total alignment",\r
-                                             annotations, 0, 10, 1);\r
+                                             annotations,\r
+                                             cons.qualityRange[0].floatValue(),\r
+                                             cons.qualityRange[1].floatValue(), 1);\r
       alignment.addAnnotation(conservation);\r
     }\r
     else\r

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 48f9c20..76559bd 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -516,7 +516,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
            height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
 \r
          }\r
-\r
+         g.setColor(row.annotations[j].colour);\r
          g.fillRect(x, y-height, av.charWidth, height );\r
        }\r
 \r