public static final String PROFILE = "P";
+ public static final String PAIRPROFILE = "B";
+
public static final Hashtable[] calculate(Vector sequences, int start,
int end)
{
maxResidue = "";
nongap = 0;
values = new int[255];
-
for (j = 0; j < jSize; j++)
{
- if (sequences[j]==null)
+ if (sequences[j] == null)
{
- System.err.println("WARNING: Consensus skipping null sequence - possible race condition.");
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
seq = sequences[j].getSequence();
result[i] = residueHash;
}
}
-
- public static int findPair(SequenceFeature[] pairs,int indice){
- for(int i=0; i<pairs.length; i++){
- if(pairs[i].getBegin()==indice){
- return pairs[i].getEnd();
- }
- }
- return -1;
+
+ public static int findPair(SequenceFeature[] pairs, int indice)
+ {
+ for (int i = 0; i < pairs.length; i++)
+ {
+ if (pairs[i].getBegin() == indice)
+ {
+ return pairs[i].getEnd();
+ }
+ }
+ return -1;
}
-
+
/**
- * Method to calculate a 'base pair consensus row', very similar
- * to nucleotide consensus but takes into account a given structure
+ * Method to calculate a 'base pair consensus row', very similar to nucleotide
+ * consensus but takes into account a given structure
+ *
* @param sequences
* @param start
* @param end
* @param rnaStruc
*/
public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result, boolean profile, AlignmentAnnotation rnaStruc){
- //System.out.println("StructureFrequency.calculateNEW4");
- Hashtable residueHash;
- String maxResidue;
- char[] seq, struc=rnaStruc.getRNAStruc().toCharArray();
- SequenceFeature[] rna =rnaStruc._rnasecstr;
- char c,s,cEnd;
- int count,nonGap=0,i,bpEnd=-1,j,jSize = sequences.length;
- int[] values = new int[255];
- float percentage;
-
- for (i = start; i < end; i++) //foreach column
- {
- residueHash = new Hashtable();
- maxResidue="-";
- values = new int[255];
- bpEnd=-1;
-
- s = struc[i];
- if (s == '.' || s == ' ')
- {
- s = '-';
- }
-
- if(s != '('){
- if(s == '-'){
- values['-']++;
- }
- }
- else
- {
- for (j = 0; j < jSize; j++) //foreach row
- {
- 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];
-
- //standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
- continue;
- }
- bpEnd=findPair(rna,i);
- cEnd=seq[bpEnd];
- if(checkBpType(c,cEnd)){
- values['H']++; //H means it's a helix (structured)
- }
- maxResidue="H";
- }
- }
-// nonGap++;
- }
- //UPDATE this for new values
- if (profile)
- {
- //System.out.println("profile");
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, values['H'] } });
- }
-
-
- count=values['H'];
-
- residueHash.put(MAXCOUNT, new Integer(count));
- residueHash.put(MAXRESIDUE, maxResidue);
-
- percentage = ((float) count * 100) / (float) jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
-
- //percentage = ((float) count * 100) / (float) nongap;
- //residueHash.put(PID_NOGAPS, new Float(percentage));
- if(result[i]==null){
- result[i] = residueHash;
- }
- if(bpEnd>0){
- result[bpEnd]=residueHash;
- }
- }
+ int end, Hashtable[] result, boolean profile,
+ AlignmentAnnotation rnaStruc)
+ {
+ // System.out.println("StructureFrequency.calculateNEW4");
+ Hashtable residueHash;
+ String maxResidue;
+ char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ SequenceFeature[] rna = rnaStruc._rnasecstr;
+ char c, s, cEnd;
+ int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int[] values;
+ int[][] pairs;
+ float percentage;
+
+ for (i = start; i < end; i++) // foreach column
+ {
+ residueHash = new Hashtable();
+ maxResidue = "-";
+ values = new int[255];
+ pairs = new int[255][255];
+ bpEnd = -1;
+
+ s = struc[i];
+ if (s == '.' || s == ' ')
+ {
+ s = '-';
+ }
+
+ if (s != '(')
+ {
+ if (s == '-')
+ {
+ values['-']++;
+ }
+ }
+ else
+ {
+ for (j = 0; j < jSize; j++) // foreach row
+ {
+ 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];
+
+ // standard representation for gaps in sequence and structure
+ if (c == '.' || c == ' ')
+ {
+ c = '-';
+ }
+
+ if (c == '-')
+ {
+ values['-']++;
+ continue;
+ }
+ bpEnd = findPair(rna, i);
+ cEnd = seq[bpEnd];
+ if (checkBpType(c, cEnd))
+ {
+ values['H']++; // 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";
+ }
+ }
+ // 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'];
+
+ residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXRESIDUE, maxResidue);
+
+ percentage = ((float) count * 100) / (float) jSize;
+ residueHash.put(PID_GAPS, new Float(percentage));
+
+ // percentage = ((float) count * 100) / (float) nongap;
+ // residueHash.put(PID_NOGAPS, new Float(percentage));
+ if (result[i] == null)
+ {
+ result[i] = residueHash;
+ }
+ if (bpEnd > 0)
+ {
+ result[bpEnd] = residueHash;
+ }
+ }
}
-
/**
- * Method to check if a base-pair is a canonical or a wobble bp
- * @param up 5' base
- * @param down 3' base
+ * Method to check if a base-pair is a canonical or a wobble bp
+ *
+ * @param up
+ * 5' base
+ * @param down
+ * 3' base
* @return True if it is a canonical/wobble bp
*/
- public static boolean checkBpType(char up, char down){
- if(up>'Z'){up-=32;}
- if(down>'Z'){down-=32;}
-
- switch (up){
- case 'A':
- switch (down){
- case 'T': return true;
- case 'U': return true;
- }
- break;
- case 'C':
- switch (down){
- case 'G': return true;
- }
- break;
- case 'T':
- switch (down){
- case 'A': return true;
- case 'G': return true;
- }
- break;
- case 'G':
- switch (down){
- case 'C': return true;
- case 'T': return true;
- case 'U': return true;
- }
- break;
- case 'U':
- switch (down){
- case 'A': return true;
- case 'G': return true;
- }
- break;
- }
- return false;
+ public static boolean checkBpType(char up, char down)
+ {
+ if (up > 'Z')
+ {
+ up -= 32;
+ }
+ if (down > 'Z')
+ {
+ down -= 32;
+ }
+
+ switch (up)
+ {
+ case 'A':
+ switch (down)
+ {
+ case 'T':
+ return true;
+ case 'U':
+ return true;
+ }
+ break;
+ case 'C':
+ switch (down)
+ {
+ case 'G':
+ return true;
+ }
+ break;
+ case 'T':
+ switch (down)
+ {
+ case 'A':
+ return true;
+ case 'G':
+ return true;
+ }
+ break;
+ case 'G':
+ switch (down)
+ {
+ case 'C':
+ return true;
+ case 'T':
+ return true;
+ case 'U':
+ return true;
+ }
+ break;
+ case 'U':
+ switch (down)
+ {
+ case 'A':
+ return true;
+ case 'G':
+ return true;
+ }
+ break;
+ }
+ return false;
}
-
+
/**
* Compute all or part of the annotation row from the given consensus
* hashtable
{
completeConsensus(consensus, hconsensus, iStart, width,
ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
- // char[]
+ // char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols, char[] alphabet)
{
- System.out.println("StructureFrequency.completeConsensus "+includeAllConsSymbols);
+ System.out.println("StructureFrequency.completeConsensus "
+ + includeAllConsSymbols);
float tval, value;
if (consensus == null || consensus.annotations == null
|| consensus.annotations.length < width)
value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS))
.floatValue();
}
-
- String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE).toString();
- String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE) + " ";
+
+ String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
+ .toString();
+ String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
+ + " ";
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
- int[][] profile = (int[][]) hconsensus[i].get(StructureFrequency.PROFILE);
- if (profile != null && includeAllConsSymbols) //Just responsible for the tooltip
+ int[][] profile = (int[][]) hconsensus[i]
+ .get(StructureFrequency.PROFILE);
+ if (profile != null && includeAllConsSymbols) // Just responsible for the
+ // tooltip
{
- //System.out.println("StructureFrequency.includeAllConsSymbols");
+ // System.out.println("StructureFrequency.includeAllConsSymbols");
mouseOver = "";
if (alphabet != null)
{
}
else
{
- //System.out.println("StructureFrequency.NOTincludeAllConsSymbols");
+ // 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++)
* @return
*/
public static int[] extractProfile(Hashtable hconsensus,
- boolean ignoreGapsInConsensusCalculation,
- int column)
+ boolean ignoreGapsInConsensusCalculation, int column)
{
- //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[22];
- int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
- if (profile == null)
- return null;
-
- Object[] ca = new Object[profile[0].length];
- float[] vl = new float[profile[0].length];
- for (int c = 0; c < ca.length; c++)
- {
- ca[c] = new char[]
- { (char) c };
- vl[c] = (float) profile[0][c];
- }
- ;
- jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 1;
- for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
- {
- if (((char[]) ca[c])[0] != '-')
- {
- rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
- //System.out.println("rtnval-"+c+": "+((char[]) ca[c])[0]);
- rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0]);
- }
- }
- for(int i=0; i<rtnval.length;i++){
- // System.out.print(rtnval[i]+",");
- }
- System.out.print("\n");
- return rtnval;
+ // 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[][] 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++)
+ {
+ for (int k = 65; k <= 90; k++)
+ {
+ 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]);
+ }
+ }
+ }
+
+ return rtnval;
}
- public static void main(String args[]){
- //Short test to see if checkBpType works
- ArrayList<String> test = new ArrayList<String>();
- test.add("A");
- test.add("c");
- test.add("g");
- test.add("T");
- test.add("U");
- for (String i : test) {
- for (String j : test) {
- System.out.println(i+"-"+j+": "+StructureFrequency.checkBpType(i.charAt(0),j.charAt(0)));
- }
- }
+ public static void main(String args[])
+ {
+ // Short test to see if checkBpType works
+ ArrayList<String> test = new ArrayList<String>();
+ test.add("A");
+ test.add("c");
+ test.add("g");
+ test.add("T");
+ test.add("U");
+ for (String i : test)
+ {
+ for (String j : test)
+ {
+ System.out.println(i + "-" + j + ": "
+ + StructureFrequency.checkBpType(i.charAt(0), j.charAt(0)));
+ }
+ }
}
}
git://source.jalview.org / jalview.git / commitdiff