/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.util.Format;
import jalview.datamodel.*;
/**
*/
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 count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
-
+ boolean wooble = true;
for (i = start; i < end; i++) // foreach column
{
residueHash = new Hashtable();
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 != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
}
else
{
+
bpEnd = findPair(rna, i);
- if (bpEnd>-1)
- {
- for (j = 0; j < jSize; j++) // foreach row
+
+ if (bpEnd > -1)
{
- if (sequences[j] == null)
- {
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
- continue;
- }
- c = sequences[j].getCharAt(i);
+ for (j = 0; j < jSize; j++) // foreach row
{
+ if (sequences[j] == null)
+ {
+ System.err
+ .println("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 == ' ')
continue;
}
cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
+
+ // System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd) == true)
{
values['(']++; // H means it's a helix (structured)
+ maxResidue = "(";
+ wooble = true;
+ // System.out.println("It's a pair wc");
+
+ }
+ if (checkBpType(c, cEnd) == false)
+ {
+ wooble = false;
+ values['[']++; // H means it's a helix (structured)
+ maxResidue = "[";
+
}
pairs[c][cEnd]++;
- maxResidue = "(";
}
}
- }
// nonGap++;
}
// UPDATE this for new values
residueHash.put(PAIRPROFILE, pairs);
}
-
- count = values['('];
-
+ if (wooble == true)
+ {
+ count = values['('];
+ }
+ if (wooble == false)
+ {
+ count = values['['];
+ }
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;
if (bpEnd > 0)
{
values[')'] = values['('];
+ values[']'] = values['['];
values['('] = 0;
-
+ values['['] = 0;
residueHash = new Hashtable();
- maxResidue = ")";
-
+ if (wooble == true)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = ")";
+ }
+ if (wooble == false)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = "]";
+ }
if (profile)
{
residueHash.put(PROFILE, new int[][]
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));
result[bpEnd] = residueHash;
+
}
}
}
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols)
+ 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);
- int[][] pairs = (int[][]) hconsensus[i]
- .get(StructureFrequency.PAIRPROFILE);
+ int[][] profile = (int[][]) hci.get(StructureFrequency.PROFILE);
+ int[][] pairs = (int[][]) hci.get(StructureFrequency.PAIRPROFILE);
if (pairs != null && includeAllConsSymbols) // Just responsible for the
// tooltip
{
mouseOver = "";
- /* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure?
+ /*
+ * 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)
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
{
if (vl[c] > 0)
{
- tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
- + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
+ + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval)
+ + "%";
p++;
}
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += (fmt.form(value) + "%");
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
- int[] rtnval = new int[52]; // 2*(5*5)+2
+ int[] rtnval = new int[74]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
{
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
+ rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
- rtnval[1]+=rtnval[rtnval[0]++];
+ rtnval[1] += rtnval[rtnval[0]++];
}
}
git://source.jalview.org / jalview.git / blobdiff