/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import jalview.util.Format;
-import java.util.ArrayList;
import java.util.Hashtable;
/**
* @param rnaStruc
*/
public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result, boolean profile,
+ int end, Hashtable<String, Object>[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
- Hashtable residueHash;
+ Hashtable<String, Object> residueHash;
String maxResidue;
char[] struc = rnaStruc.getRNAStruc().toCharArray();
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
- int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int bpEnd = -1;
+ int jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
- boolean wooble = true;
- 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;
- // System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
-
}
else
{
s = '-';
}
- if (s != '(' && s != '[')
+ if (!Rna.isOpeningParenthesis(s))
{
if (s == '-')
{
}
else
{
-
bpEnd = findPair(rna, i);
if (bpEnd > -1)
{
- for (j = 0; j < jSize; j++) // foreach row
+ for (int j = 0; j < jSize; j++) // foreach row
{
if (sequences[j] == null)
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ jalview.bin.Console.errPrintln(
+ "WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- c = sequences[j].getCharAt(i);
- // System.out.println("c="+c);
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
+ c = sequences[j].getCharAt(i);
+ cEnd = sequences[j].getCharAt(bpEnd);
- if (c == '-')
+ if (Comparison.isGap(c) || Comparison.isGap(cEnd))
{
values['-']++;
continue;
}
- cEnd = sequences[j].getCharAt(bpEnd);
-
- // System.out.println("pairs ="+c+","+cEnd);
- if (checkBpType(c, cEnd) == true)
+ nongap++;
+ /*
+ * ensure upper-case for counting purposes
+ */
+ if ('a' <= c && 'z' >= c)
{
- values['(']++; // H means it's a helix (structured)
- maxResidue = "(";
- wooble = true;
- // System.out.println("It's a pair wc");
-
+ c += 'A' - 'a';
}
- if (checkBpType(c, cEnd) == false)
+ if ('a' <= cEnd && 'z' >= cEnd)
{
- wooble = false;
- values['[']++; // H means it's a helix (structured)
- maxResidue = "[";
-
+ cEnd += 'A' - 'a';
+ }
+ if (Rna.isCanonicalOrWobblePair(c, cEnd))
+ {
+ canonicalOrWobblePairCount++;
+ if (Rna.isCanonicalPair(c, cEnd))
+ {
+ canonical++;
+ }
+ }
+ else
+ {
+ otherPairCount++;
}
pairs[c][cEnd]++;
-
}
}
- // nonGap++;
}
- // UPDATE this for new values
+
+ residueHash = new Hashtable<>();
if (profile)
{
// 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(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
- if (wooble == true)
- {
- count = values['('];
- }
- if (wooble == false)
+ 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)
{
- count = values['['];
+ if (canonicalOrWobblePairCount >= otherPairCount)
+ {
+ maxResidue = (canonicalOrWobblePairCount - canonical) < canonical
+ ? "("
+ : "[";
+ }
+ else
+ {
+ maxResidue = "{";
+ }
}
- residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXCOUNT, Integer.valueOf(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
+ residueHash.put(PID_GAPS, Float.valueOf(percentage));
+
+ percentage = ((float) count * 100) / nongap;
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
- // percentage = ((float) count * 100) / (float) nongap;
- // residueHash.put(PID_NOGAPS, new Float(percentage));
if (result[i] == null)
{
result[i] = residueHash;
{
values[')'] = values['('];
values[']'] = values['['];
+ values['}'] = values['{'];
values['('] = 0;
values['['] = 0;
- residueHash = new Hashtable();
- if (wooble == true)
- {
- // System.out.println(maxResidue+","+wooble);
- maxResidue = ")";
- }
- if (wooble == false)
- {
- // System.out.println(maxResidue+","+wooble);
- maxResidue = "]";
- }
+ values['{'] = 0;
+ maxResidue = maxResidue.equals("(") ? ")"
+ : maxResidue.equals("[") ? "]" : "}";
+
+ residueHash = new Hashtable<>();
if (profile)
{
- residueHash.put(PROFILE, new int[][] { values,
- new int[] { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
- residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXCOUNT, Integer.valueOf(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
-
- result[bpEnd] = residueHash;
-
- }
- }
- }
+ residueHash.put(PID_GAPS, Float.valueOf(percentage));
- /**
- * 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;
- }
+ percentage = ((float) count * 100) / nongap;
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
- 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;
+ result[bpEnd] = residueHash;
}
- break;
}
- return false;
}
/**
* @param includeAllConsSymbols
*/
public static void completeConsensus(AlignmentAnnotation consensus,
- Hashtable[] hconsensus, int iStart, int width,
+ Hashtable<String, Object>[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols, long nseq)
{
for (int i = iStart; i < width; i++)
{
- Hashtable hci;
+ Hashtable<String, Object> hci;
if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
{
// happens if sequences calculated over were shorter than alignment
* @param hconsensus
* @return profile of the given column
*/
- public static int[] extractProfile(Hashtable hconsensus,
+ public static int[] extractProfile(Hashtable<String, Object> hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
int[] rtnval = new int[STRUCTURE_PROFILE_LENGTH]; // 2*(5*5)+2
int valuesCount = 0;
rtnval[1] = 0;
int offset = 2;
- final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
System.arraycopy(rtnval, 0, result, 1, rtnval.length);
return result;
}
-
- 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 / blobdiff