/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
+
package jalview.analysis;
import java.util.*;
public static final String PAIRPROFILE = "B";
- public static final Hashtable[] calculate(Vector sequences, int start,
- int end)
- {
- return calculate(sequences, start, end, false);
- }
-
- public static final Hashtable[] calculate(Vector sequences, int start,
- int end, boolean profile)
- {
- SequenceI[] seqs = new SequenceI[sequences.size()];
- int width = 0;
- for (int i = 0; i < sequences.size(); i++)
- {
- seqs[i] = (SequenceI) sequences.elementAt(i);
- if (seqs[i].getLength() > width)
- {
- width = seqs[i].getLength();
- }
- }
-
- Hashtable[] reply = new Hashtable[width];
-
- if (end >= width)
- {
- end = width;
- }
-
- calculate(seqs, start, end, reply, profile);
-
- return reply;
- }
-
- public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result)
- {
- calculate(sequences, start, end, result, false);
- }
-
- public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result, boolean profile)
- {
- Hashtable residueHash;
- int maxCount, nongap, i, j, v, jSize = sequences.length;
- String maxResidue;
- char c;
- float percentage;
-
- int[] values = new int[255];
-
- char[] seq;
-
- for (i = start; i < end; i++)
- {
- residueHash = new Hashtable();
- maxCount = 0;
- maxResidue = "";
- nongap = 0;
- values = new int[255];
-
- for (j = 0; j < jSize; j++)
- {
- if (sequences[j] == null)
- {
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
- continue;
- }
- seq = sequences[j].getSequence();
- if (seq.length > i)
- {
- c = seq[i];
-
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
- continue;
- }
- else if ('a' <= c && c <= 'z')
- {
- c -= 32; // ('a' - 'A');
- }
-
- nongap++;
- values[c]++;
-
- }
- else
- {
- values['-']++;
- }
- }
-
- for (v = 'A'; v < 'Z'; v++)
- {
- if (values[v] < 2 || values[v] < maxCount)
- {
- continue;
- }
-
- if (values[v] > maxCount)
- {
- maxResidue = String.valueOf((char) v);
- }
- else if (values[v] == maxCount)
- {
- maxResidue += String.valueOf((char) v);
- }
- maxCount = values[v];
- }
-
- if (maxResidue.length() == 0)
- {
- maxResidue = "-";
- }
- if (profile)
- {
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, nongap } });
- }
- residueHash.put(MAXCOUNT, new Integer(maxCount));
- residueHash.put(MAXRESIDUE, maxResidue);
-
- percentage = ((float) maxCount * 100) / (float) jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
-
- percentage = ((float) maxCount * 100) / (float) nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
- result[i] = residueHash;
- }
- }
-
+ /**
+ * Returns the 3' position of a base pair
+ *
+ * @param pairs
+ * Secondary structure annotation
+ * @param indice
+ * 5' position of a base pair
+ * @return 3' position of a base pair
+ */
public static int findPair(SequenceFeature[] pairs, int indice)
{
for (int i = 0; i < pairs.length; i++)
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
- // System.out.println("StructureFrequency.calculateNEW4");
Hashtable residueHash;
String maxResidue;
char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
-
- s = struc[i];
+ if (i < struc.length)
+ {
+ s = struc[i];
+ }
+ else
+ {
+ s = '-';
+ }
if (s == '.' || s == ' ')
{
s = '-';
cEnd = seq[bpEnd];
if (checkBpType(c, cEnd))
{
- values['H']++; // H means it's a helix (structured)
+ values['(']++; // H means it's a helix (structured)
}
- // System.out.println("pair: "+c+","+cEnd);
pairs[c][cEnd]++;
- // System.out.println("pairs: "+c+","+cEnd+" - "+pairs[c][cEnd]);
- maxResidue = "H";
+ maxResidue = "(";
}
}
// nonGap++;
// UPDATE this for new values
if (profile)
{
- // System.out.println("profile");
residueHash.put(PROFILE, new int[][]
{ values, new int[]
{ jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
- count = values['H'];
+ count = values['('];
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
}
if (bpEnd > 0)
{
+ values[')'] = values['('];
+ values['('] = 0;
+
+ residueHash = new Hashtable();
+ maxResidue = ")";
+
+ if (profile)
+ {
+ residueHash.put(PROFILE, new int[][]
+ { values, new int[]
+ { jSize, (jSize - values['-']) } });
+
+ residueHash.put(PAIRPROFILE, pairs);
+ }
+
+ residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXRESIDUE, maxResidue);
+
+ percentage = ((float) count * 100) / (float) jSize;
+ residueHash.put(PID_GAPS, new Float(percentage));
+
result[bpEnd] = residueHash;
}
}
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols)
{
- completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
- // char[]
- // { 'A', 'C', 'G', 'T', 'U' });
- }
-
- public static void completeConsensus(AlignmentAnnotation consensus,
- Hashtable[] hconsensus, int iStart, int width,
- boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols, char[] alphabet)
- {
- System.out.println("StructureFrequency.completeConsensus "
- + includeAllConsSymbols);
float tval, value;
if (consensus == null || consensus.annotations == null
|| consensus.annotations.length < width)
}
int[][] profile = (int[][]) hconsensus[i]
.get(StructureFrequency.PROFILE);
- if (profile != null && includeAllConsSymbols) // Just responsible for the
+ int[][] pairs = (int[][]) hconsensus[i]
+ .get(StructureFrequency.PAIRPROFILE);
+
+ if (pairs != null && includeAllConsSymbols) // Just responsible for the
// tooltip
+ // TODO Update tooltips for Structure row
{
- // System.out.println("StructureFrequency.includeAllConsSymbols");
mouseOver = "";
- if (alphabet != null)
+
+ /* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure?
+ *
+ * if (alphabet != null) { for (int c = 0; c < alphabet.length; c++) {
+ * tval = ((float) profile[0][alphabet[c]]) 100f / (float)
+ * profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver +=
+ * ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; } }
+ * else {
+ */
+ Object[] ca = new Object[625];
+ float[] vl = new float[625];
+ int x = 0;
+ for (int c = 65; c < 90; c++)
{
- for (int c = 0; c < alphabet.length; c++)
+ for (int d = 65; d < 90; d++)
{
- tval = ((float) profile[0][alphabet[c]])
- * 100f
- / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0];
- mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + ((int) tval) + "%";
+ ca[x] = new int[]
+ { c, d };
+ vl[x] = (float) pairs[c][d];
+ x++;
}
}
- else
+ jalview.util.QuickSort.sort(vl, ca);
+ int p = 0;
+
+ for (int c = 624; c > 0; c--)
{
- // System.out.println("StructureFrequency.NOTincludeAllConsSymbols");
- Object[] ca = new Object[profile[0].length];
- float[] vl = new float[profile[0].length];
- for (int c = 0; c < ca.length; c++)
+ if (vl[c] > 0)
{
- ca[c] = new char[]
- { (char) c };
- vl[c] = (float) profile[0][c];
- }
- ;
- jalview.util.QuickSort.sort(vl, ca);
- for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
- {
- if (((char[]) ca[c])[0] != '-')
- {
- tval = ((float) profile[0][((char[]) ca[c])[0]])
- * 100f
- / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0];
- mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + ((int) tval) + "%";
- p++;
+ tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0]);
+ mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
+ + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
+ p++;
- }
}
-
}
+
+ // }
}
else
{
}
/**
- * get the sorted profile for the given position of the consensus
+ * get the sorted base-pair profile for the given position of the consensus
*
* @param hconsensus
- * @return
+ * @return profile of the given column
*/
public static int[] extractProfile(Hashtable hconsensus,
- boolean ignoreGapsInConsensusCalculation, int column)
+ boolean ignoreGapsInConsensusCalculation)
{
- // TODO is there a more elegant way to acces the column number?
- /*
- * calculate the frequence of the 16 bp variations for this column 'somehow'
- * transfer this via getProfile and let it correctly draw
- */
- int[] rtnval = new int[51]; // 2*(5*5)+1
+ int[] rtnval = new int[52]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
if (profile == null)
return null;
-
- rtnval[0] = 1;
- for (int j = 65; j <= 90; j++)
+
+ // TODO fix the object length, also do it in completeConsensus
+ Object[] ca = new Object[625];
+ float[] vl = new float[625];
+ int x = 0;
+ for (int c = 65; c < 90; c++)
{
- for (int k = 65; k <= 90; k++)
+ for (int d = 65; d < 90; d++)
{
- if (pairs[j][k] > 0)
- {
- rtnval[rtnval[0]++] = j;
- rtnval[rtnval[0]++] = k;
- rtnval[rtnval[0]++] = (int) ((float) pairs[j][k] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0]);
- }
+ ca[x] = new int[]
+ { c, d };
+ vl[x] = (float) pairs[c][d];
+ x++;
+ }
+ }
+ jalview.util.QuickSort.sort(vl, ca);
+
+ rtnval[0] = 2;
+ rtnval[1] = 0;
+ for (int c = 624; c > 0; c--)
+ {
+ if (vl[c] > 0)
+ {
+ rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
+ rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
+ rtnval[rtnval[0]] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0]);
+ rtnval[1]+=rtnval[rtnval[0]++];
}
}
git://source.jalview.org / jalview.git / blobdiff