X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=1f6f4236219b531a27131f928defe9bd5807037a;hb=95a46891288f4fc63d690cab4f56879678f54fb6;hp=8110c48e22d01c25a03c0495f94b0569780dc18a;hpb=a1d70e0b90e00b1908d43986093fe1b6b9c65fde;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 8110c48..1f6f423 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -25,44 +25,70 @@ import jalview.datamodel.*;
 import java.util.*;
 
 
-public class AAFrequency {
-    // Takes in a vector of sequences and column start and column end
-    // and returns a vector of size (end-start+1). Each element of the
-    // vector contains a hashtable with the keys being residues and
-    // the values being the count of each residue in that column.
-    // This class is used extensively in calculating alignment colourschemes
-    // that depend on the amount of conservation in each alignment column.
-    public static Vector calculate(Vector sequences, int start, int end) {
-        Vector result = new Vector();
-
-        for (int i = start; i <= end; i++) {
-            Hashtable residueHash = new Hashtable();
-            int maxCount = 0;
-            String maxResidue = "-";
-            int nongap = 0;
-
-            for (int j = 0; j < sequences.size(); j++) {
-                if (sequences.elementAt(j) instanceof Sequence) {
-                    Sequence s = (Sequence) sequences.elementAt(j);
-
-                    if (s.getSequence().length() > i) {
-                        String res = s.getSequence().charAt(i) + "";
-
-                        if (!jalview.util.Comparison.isGap(res.charAt(0))) {
-                            nongap++;
-                        } else {
+/**
+ * Takes in a vector of sequences and column start and column end
+ * and returns a vector of size (end-start+1). Each element of the
+ * vector contains a hashtable with the keys being residues and
+ * the values being the count of each residue in that column.
+ * This class is used extensively in calculating alignment colourschemes
+ * that depend on the amount of conservation in each alignment column.
+ * @author $author$
+ * @version $Revision$
+ */
+public class AAFrequency
+{
+    /** Takes in a vector of sequences and column start and column end
+    * and returns a vector of size (end-start+1). Each element of the
+    * vector contains a hashtable with the keys being residues and
+    * the values being the count of each residue in that column.
+    * This class is used extensively in calculating alignment colourschemes
+    * that depend on the amount of conservation in each alignment column. */
+    public static Vector calculate(Vector sequences, int start, int end)
+    {
+      Vector result = new Vector();
+      Hashtable residueHash;
+      int count, maxCount, nongap, i, j, jSize = sequences.size();
+      String maxResidue, sequence, res;
+      float percentage;
+
+        for (i = start; i <= end; i++)
+        {
+            residueHash = new Hashtable();
+            maxCount = 0;
+            maxResidue = "-";
+            nongap = 0;
+
+            for (j = 0; j < jSize; j++)
+            {
+                if (sequences.elementAt(j) instanceof Sequence)
+                {
+                    sequence = ((Sequence) sequences.elementAt(j)).getSequence();
+
+                    if (sequence.length() > i)
+                    {
+                        res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
+
+                        if (jalview.util.Comparison.isGap(res.charAt(0)))
+                        {
                             res = "-"; // we always use this for gaps in the property vectors
                         }
+                        else
+                        {   nongap++;    }
 
-                        if (residueHash.containsKey(res)) {
-                            int count = ((Integer) residueHash.get(res)).intValue();
+                        if (residueHash.containsKey(res))
+                        {
+                            count = ((Integer) residueHash.get(res)).intValue();
                             count++;
 
                             if (!jalview.util.Comparison.isGap(res.charAt(0)) &&
-                                    (count >= maxCount)) {
-                                if (count > maxCount) {
+                                    (count >= maxCount))
+                            {
+                                if (count > maxCount)
+                                {
                                     maxResidue = res;
-                                } else if (maxResidue.indexOf(res) == -1) {
+                                }
+                                else if (maxResidue.indexOf(res) == -1)
+                                {
                                     maxResidue += res;
                                 }
 
@@ -70,15 +96,22 @@ public class AAFrequency {
                             }
 
                             residueHash.put(res, new Integer(count));
-                        } else {
+                        }
+                        else
+                        {
                             residueHash.put(res, new Integer(1));
                         }
-                    } else {
-                        if (residueHash.containsKey("-")) {
-                            int count = ((Integer) residueHash.get("-")).intValue();
+                    }
+                    else
+                    {
+                        if (residueHash.containsKey("-"))
+                        {
+                            count = ((Integer) residueHash.get("-")).intValue();
                             count++;
                             residueHash.put("-", new Integer(count));
-                        } else {
+                        }
+                        else
+                        {
                             residueHash.put("-", new Integer(1));
                         }
                     }
@@ -86,292 +119,23 @@ public class AAFrequency {
             }
 
             residueHash.put("maxCount", new Integer(maxCount));
-
-            if (maxCount < 0) {
-                System.out.println("asasa " + maxCount);
-            }
-
             residueHash.put("maxResidue", maxResidue);
-            residueHash.put("size", new Integer(sequences.size()));
-            residueHash.put("nongap", new Integer(nongap));
-            result.addElement(residueHash);
-        }
-
-        return result;
-    }
-
-    public static Vector calculatePID(SequenceI refseq, Vector sequences,
-        int window, int start, int end) {
-        Vector result = new Vector();
-
-        boolean init = true;
-
-        Vector prev = null;
-
-        for (int i = start; i <= end; i++) {
-            Vector values = new Vector();
-
-            result.addElement(values);
-
-            // If start < window/2 then set value to zero.
-            if ((i < (window / 2)) ||
-                    (i >= (refseq.getSequence().length() - (window / 2)))) {
-                for (int j = 0; j < sequences.size(); j++) {
-                    values.addElement(new Integer(0));
-                }
-            } else if (init == true) {
-                init = false;
-
-                int winstart = i - (window / 2);
-                int winend = i + (window / 2);
-
-                if ((window % 2) != 0) {
-                    winend++;
-                }
-
-                for (int j = 0; j < sequences.size(); j++) {
-                    values.addElement(new Integer(0));
-                }
-
-                for (int k = winstart; k <= winend; k++) {
-                    String refchar = refseq.getSequence().substring(k, k + 1);
-
-                    if (jalview.util.Comparison.isGap(refchar.charAt(0))) {
-                        refchar = "-";
-                    } else {
-                        for (int j = 0; j < sequences.size(); j++) {
-                            Sequence s = (Sequence) sequences.elementAt(j);
 
-                            if (s.getSequence().length() > k) {
-                                String res = s.getSequence().substring(k, k +
-                                        1); // no gapchar test needed
-
-                                if (res.equals(refchar)) {
-                                    int val = ((Integer) values.elementAt(j)).intValue();
-                                    val++;
-                                    values.setElementAt(new Integer(val), j);
-                                }
-                            }
-                        }
-                    }
-                }
-
-                prev = values;
-            } else {
-                int winstart = i - (window / 2);
-                int winend = i + (window / 2);
-
-                if ((window % 2) != 0) {
-                    winend++;
-                }
-
-                // We need to take the previous set of values
-                // subtract the pid at winstart-1
-                // and add the pid at winend;
-                String pre_refchar = refseq.getSequence().substring(winstart -
-                        1, winstart);
-                String pos_refchar = "-";
-
-                if (refseq.getSequence().length() > winend) {
-                    pos_refchar = refseq.getSequence().substring(winend,
-                            winend + 1);
-                }
-
-                for (int j = 0; j < sequences.size(); j++) {
-                    // First copy the pid value from i-1
-                    int val = ((Integer) prev.elementAt(j)).intValue();
-
-                    Sequence s = (Sequence) sequences.elementAt(j);
-
-                    String pre_char = s.getSequence().substring(winstart - 1,
-                            winstart);
-
-                    String pos_char = "-";
-
-                    if (s.getSequence().length() > winend) {
-                        pos_char = s.getSequence().substring(winend, winend +
-                                1);
-                    }
-
-                    // Now substract 1 if the chars at winstart-1 match
-                    if ((jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false) &&
-                            pre_char.equals(pre_refchar)) {
-                        val--;
-                    }
-
-                    if ((jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false) &&
-                            pos_char.equals(pos_refchar)) {
-                        val++;
-                    }
-
-                    values.addElement(new Integer(val));
-                }
-
-                prev = values;
-            }
-        }
-
-        return result;
-    }
 
-    public static Hashtable findBlocks(Vector seqs, int start, int end,
-        Vector exc) {
-        // start and end are in real (not relative coords);
-        // The coords in the hashtable that is returned are in relative coords
-        // i.e. start from 0
-        Hashtable blocks = new Hashtable();
+            //Size is redundant at present if we calculate percentage here
+            //residueHash.put("size", new Integer(jSize));
+            //residueHash.put("nogaps", new Integer(nongap));
 
-        boolean prev = false;
-        int bstart = -1;
+            percentage = ((float)maxCount*100) / (float)jSize;
+            residueHash.put("pid_gaps", new Float(percentage) );
 
-        for (int i = start; i <= end; i++) {
-            SequenceI seq = (SequenceI) seqs.elementAt(0);
-
-            char c = seq.getCharAt(i);
-
-            boolean found = true;
-
-            int j = 1;
-
-            while ((j < seqs.size()) && (found == true)) {
-                SequenceI jseq = (SequenceI) seqs.elementAt(j);
-
-                if (!exc.contains(jseq)) {
-                    char cc = jseq.getCharAt(i);
-
-                    if (cc != c) {
-                        found = false;
-                    }
-                }
-
-                j++;
-            }
-
-            if ((prev == false) && (found == true)) {
-                bstart = i;
-            } else if ((prev == true) && (found == false) && (bstart != -1)) {
-                int blockstart = bstart - start;
-                int blocklen = i - bstart;
-
-                //System.out.println("Start len " + blockstart + " " + blocklen);
-                for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {
-                    blocks.put(new Integer(jj), new Integer(blocklen));
-                }
-
-                bstart = -1;
-            }
-
-            prev = found;
-        }
-
-        if (bstart != -1) {
-            int blockstart = bstart - start;
-            int blocklen = end - bstart;
-
-            //  System.out.println("Start len " + blockstart + " " + blocklen);
-            for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {
-                blocks.put(new Integer(blockstart), new Integer(blocklen));
-            }
-        }
-
-        return blocks;
-    }
-
-    public static Hashtable findKmerCount(SequenceI seq, int start, int end,
-        int window, int step, Vector kmers) {
-        int tmpstart = start;
-        Hashtable vals = new Hashtable();
-
-        while (tmpstart <= end) {
-            String tmpstr = seq.getSequence().substring(tmpstart -
-                    (window / 2), tmpstart + (window / 2));
-
-            int count = 0;
-
-            //System.out.println("Str " + tmpstr);
-            for (int ii = 0; ii < kmers.size(); ii++) {
-                String kmer = ((SequenceI) kmers.elementAt(ii)).getSequence();
-
-                int i = -1;
-
-                while (tmpstr.indexOf(kmer, i) != -1) {
-                    i = tmpstr.indexOf(kmer, i);
-
-                    i++;
-                    count++;
-                }
-
-                ii++;
-            }
-
-            vals.put(new Integer(tmpstart), new Integer(count));
-            tmpstart += step;
-        }
-
-        return vals;
-    }
-
-    public static Hashtable findBlockStarts(Vector seqs, int start, int end,
-        Vector exc) {
-        // start and end are in real (not relative coords);
-        // The coords in the hashtable that is returned are in relative coords
-        // i.e. start from 0
-        Hashtable blocks = new Hashtable();
-
-        boolean prev = false;
-        int bstart = -1;
-
-        for (int i = start; i <= end; i++) {
-            SequenceI seq = (SequenceI) seqs.elementAt(0);
-
-            char c = seq.getCharAt(i);
-
-            boolean found = true;
-
-            int j = 1;
-
-            while ((j < seqs.size()) && (found == true)) {
-                SequenceI jseq = (SequenceI) seqs.elementAt(j);
-
-                if (!exc.contains(jseq)) {
-                    char cc = jseq.getCharAt(i);
-
-                    if (cc != c) {
-                        found = false;
-                    }
-                }
-
-                j++;
-            }
-
-            if ((prev == false) && (found == true)) {
-                bstart = i;
-            } else if ((prev == true) && (found == false) && (bstart != -1)) {
-                int blockstart = bstart - start;
-                int blocklen = i - bstart;
-
-                //		System.out.println("Start len " + blockstart + " " + blocklen);
-                //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-                blocks.put(new Integer(blockstart), new Integer(blocklen));
-
-                //	}
-                bstart = -1;
-            }
-
-            prev = found;
+            percentage = ((float)maxCount*100) / (float)nongap;
+            residueHash.put("pid_nogaps", new Float(percentage) );
+            result.addElement(residueHash);
         }
 
-        if (bstart != -1) {
-            int blockstart = bstart - start;
-            int blocklen = end - bstart;
 
-            //  System.out.println("Start len " + blockstart + " " + blocklen);
-            //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-            blocks.put(new Integer(blockstart), new Integer(blocklen));
 
-            // }
-        }
-
-        return blocks;
+        return result;
     }
 }