X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=dc0212e9f255e20f47519d000c1ac4050921eb35;hb=a38b2227929a7eb5dee0925cb4c57d43d383718f;hp=948bdc134dfaf06dbb15d29df177cc1010fd2c52;hpb=948228d480dcd77e194de69b393dfe5f29f51bb3;p=jalview.git
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 948bdc1..dc0212e 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,22 +1,23 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
-
package jalview.analysis;
import java.util.*;
@@ -60,11 +61,15 @@ public class StructureFrequency
*/
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;
@@ -85,16 +90,18 @@ public class StructureFrequency
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();
@@ -102,9 +109,11 @@ public class StructureFrequency
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
{
@@ -115,7 +124,7 @@ public class StructureFrequency
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
@@ -124,7 +133,9 @@ public class StructureFrequency
}
else
{
+
bpEnd = findPair(rna, i);
+
if (bpEnd > -1)
{
for (j = 0; j < jSize; j++) // foreach row
@@ -136,28 +147,39 @@ public class StructureFrequency
continue;
}
c = sequences[j].getCharAt(i);
+ // System.out.println("c="+c);
+
+ // standard representation for gaps in sequence and structure
+ if (c == '.' || c == ' ')
{
+ c = '-';
+ }
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
- continue;
- }
- cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
- {
- values['(']++; // H means it's a helix (structured)
- }
- pairs[c][cEnd]++;
+ if (c == '-')
+ {
+ values['-']++;
+ continue;
+ }
+ cEnd = sequences[j].getCharAt(bpEnd);
+ // 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]++;
+
}
}
// nonGap++;
@@ -171,9 +193,14 @@ public class StructureFrequency
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);
@@ -189,11 +216,20 @@ public class StructureFrequency
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[][]
@@ -210,6 +246,7 @@ public class StructureFrequency
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
@@ -310,18 +347,19 @@ public class StructureFrequency
// initialised properly
return;
}
- String fmtstr="%3.1f";
- int precision=2;
- while (nseq>100) {
+ String fmtstr = "%3.1f";
+ int precision = 2;
+ while (nseq > 100)
+ {
precision++;
- nseq/=10;
+ nseq /= 10;
}
- if (precision>2)
+ if (precision > 2)
{
- fmtstr = "%"+(2+precision)+"."+precision+"f";
+ fmtstr = "%" + (2 + precision) + "." + precision + "f";
}
Format fmt = new Format(fmtstr);
-
+
for (int i = iStart; i < width; i++)
{
Hashtable hci;
@@ -398,7 +436,8 @@ public class StructureFrequency
tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
- + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval) + "%";
+ + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval)
+ + "%";
p++;
}