/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+import jalview.util.Format;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
/**
* Takes in a vector or array of sequences and column start and column end and
*/
public class StructureFrequency
{
+ public static final int STRUCTURE_PROFILE_LENGTH = 74;
+
// No need to store 1000s of strings which are not
// visible to the user.
public static final String MAXCOUNT = "C";
public static final String PAIRPROFILE = "B";
-/**
- * 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
- */
+ /**
+ * 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++)
{
if (pairs[i].getBegin() == indice)
+
{
+
return pairs[i].getEnd();
+
}
}
return -1;
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
+
Hashtable residueHash;
String maxResidue;
- char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ char[] struc = rnaStruc.getRNAStruc().toCharArray();
+
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
- int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int bpEnd = -1;
+ int jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
- for (i = start; i < end; i++) // foreach column
+ for (int i = start; i < end; i++) // foreach column
{
- residueHash = new Hashtable();
+ int canonicalOrWobblePairCount = 0, canonical = 0;
+ int otherPairCount = 0;
+ int nongap = 0;
maxResidue = "-";
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 = '-';
}
- if (s != '(')
+ if (!Rna.isOpeningParenthesis(s))
{
if (s == '-')
{
}
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();
+ bpEnd = findPair(rna, i);
- if (seq.length > i)
+ if (bpEnd > -1)
+ {
+ for (int j = 0; j < jSize; j++) // foreach row
{
- c = seq[i];
-
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
+ if (sequences[j] == null)
{
- c = '-';
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
}
- if (c == '-')
+ c = sequences[j].getCharAt(i);
+ cEnd = sequences[j].getCharAt(bpEnd);
+
+ if (Comparison.isGap(c) || Comparison.isGap(cEnd))
{
values['-']++;
continue;
}
- bpEnd = findPair(rna, i);
- cEnd = seq[bpEnd];
- if (checkBpType(c, cEnd))
+ nongap++;
+ /*
+ * ensure upper-case for counting purposes
+ */
+ if ('a' <= c && 'z' >= c)
{
- values['H']++; // H means it's a helix (structured)
+ c += 'A' - 'a';
+ }
+ if ('a' <= cEnd && 'z' >= cEnd)
+ {
+ cEnd += 'A' - 'a';
+ }
+ if (Rna.isCanonicalOrWobblePair(c, cEnd))
+ {
+ canonicalOrWobblePairCount++;
+ if (Rna.isCanonicalPair(c, cEnd))
+ {
+ canonical++;
+ }
+ }
+ else
+ {
+ otherPairCount++;
}
pairs[c][cEnd]++;
-
- maxResidue = "H";
}
}
- // nonGap++;
}
- // UPDATE this for new values
+
+ residueHash = new Hashtable();
if (profile)
{
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, (jSize - values['-']) } });
+ // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
+ residueHash.put(PROFILE, new int[][] { values,
+ new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
-
- count = values['H'];
-
+ values['('] = canonicalOrWobblePairCount;
+ values['['] = canonical;
+ values['{'] = otherPairCount;
+ /*
+ * the count is the number of valid pairs (as a percentage, determines
+ * the relative size of the profile logo)
+ */
+ int count = canonicalOrWobblePairCount;
+
+ /*
+ * display '(' if most pairs are canonical, or as
+ * '[' if there are more wobble pairs.
+ */
+ if (canonicalOrWobblePairCount > 0 || otherPairCount > 0)
+ {
+ if (canonicalOrWobblePairCount >= otherPairCount)
+ {
+ maxResidue = (canonicalOrWobblePairCount - canonical) < canonical ? "("
+ : "[";
+ }
+ else
+ {
+ maxResidue = "{";
+ }
+ }
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
- percentage = ((float) count * 100) / (float) jSize;
+ percentage = ((float) count * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
- // percentage = ((float) count * 100) / (float) nongap;
- // residueHash.put(PID_NOGAPS, new Float(percentage));
+ percentage = ((float) count * 100) / nongap;
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
if (result[i] == null)
{
result[i] = residueHash;
}
if (bpEnd > 0)
{
- result[bpEnd] = residueHash;
- }
- }
- }
+ values[')'] = values['('];
+ values[']'] = values['['];
+ values['}'] = values['{'];
+ values['('] = 0;
+ values['['] = 0;
+ values['{'] = 0;
+ maxResidue = maxResidue.equals("(") ? ")"
+ : maxResidue.equals("[") ? "]" : "}";
+
+ residueHash = new Hashtable();
+ if (profile)
+ {
+ residueHash.put(PROFILE, new int[][] { values,
+ new int[] { jSize, (jSize - values['-']) } });
- /**
- * 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;
- }
+ residueHash.put(PAIRPROFILE, pairs);
+ }
- 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;
+ residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXRESIDUE, maxResidue);
+
+ percentage = ((float) count * 100) / jSize;
+ residueHash.put(PID_GAPS, new Float(percentage));
+
+ percentage = ((float) count * 100) / nongap;
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
+ result[bpEnd] = residueHash;
}
- break;
}
- return false;
}
/**
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
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)
+ boolean includeAllConsSymbols, long nseq)
{
float tval, value;
if (consensus == null || consensus.annotations == null
// initialised properly
return;
}
+ String fmtstr = "%3.1f";
+ int precision = 2;
+ while (nseq > 100)
+ {
+ precision++;
+ nseq /= 10;
+ }
+ if (precision > 2)
+ {
+ fmtstr = "%" + (2 + precision) + "." + precision + "f";
+ }
+ Format fmt = new Format(fmtstr);
+
for (int i = iStart; i < width; i++)
{
- if (i >= hconsensus.length)
+ Hashtable hci;
+ if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
{
// happens if sequences calculated over were shorter than alignment
// width
continue;
}
value = 0;
+ Float fv;
if (ignoreGapsInConsensusCalculation)
{
- value = ((Float) hconsensus[i].get(StructureFrequency.PID_NOGAPS))
- .floatValue();
+ fv = (Float) hci.get(StructureFrequency.PID_NOGAPS);
}
else
{
- value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS))
- .floatValue();
+ fv = (Float) hci.get(StructureFrequency.PID_GAPS);
}
-
- String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
- .toString();
- String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
- + " ";
+ if (fv == null)
+ {
+ consensus.annotations[i] = null;
+ // data has changed below us .. give up and
+ continue;
+ }
+ value = fv.floatValue();
+ String maxRes = hci.get(StructureFrequency.MAXRESIDUE).toString();
+ String mouseOver = hci.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
+ int[][] profile = (int[][]) hci.get(StructureFrequency.PROFILE);
+ int[][] pairs = (int[][]) hci.get(StructureFrequency.PAIRPROFILE);
+
+ if (pairs != null && includeAllConsSymbols) // Just responsible for the
// tooltip
+ // TODO Update tooltips for Structure row
{
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 {
+ */
+ int[][] ca = new int[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] = pairs[c][d];
+ x++;
}
}
- else
+ jalview.util.QuickSort.sort(vl, ca);
+ int p = 0;
+
+ /*
+ * profile[1] is {total, ungappedTotal}
+ */
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
+ for (int c = 624; c > 0; c--)
{
- 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 = (vl[c] * 100f / divisor);
+ mouseOver += ((p == 0) ? "" : "; ") + (char) ca[c][0]
+ + (char) ca[c][1] + " " + fmt.form(tval) + "%";
+ p++;
- }
}
-
}
+
+ // }
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += (fmt.form(value) + "%");
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
* @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[STRUCTURE_PROFILE_LENGTH]; // 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];
+ int[][] ca = new int[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] = pairs[c][d];
+ x++;
+ }
+ }
+ jalview.util.QuickSort.sort(vl, ca);
+
+ int valuesCount = 0;
+ rtnval[1] = 0;
+ int offset = 2;
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ for (int c = 624; c > 0; c--)
+ {
+ if (vl[c] > 0)
+ {
+ rtnval[offset++] = ca[c][0];
+ rtnval[offset++] = ca[c][1];
+ rtnval[offset] = (int) (vl[c] * 100f / divisor);
+ rtnval[1] += rtnval[offset++];
+ valuesCount++;
}
}
+ rtnval[0] = valuesCount;
- return rtnval;
+ // insert profile type code in position 0
+ int[] result = new int[rtnval.length + 1];
+ result[0] = AlignmentAnnotation.STRUCTURE_PROFILE;
+ System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+ return result;
}
public static void main(String args[])
for (String j : test)
{
System.out.println(i + "-" + j + ": "
- + StructureFrequency.checkBpType(i.charAt(0), j.charAt(0)));
+ + Rna.isCanonicalOrWobblePair(i.charAt(0), j.charAt(0)));
}
}
}
git://source.jalview.org / jalview.git / blobdiff