X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=d7d07bc282f07d5876f374a257af10d631fbd4d5;hb=fd78187d73394a2a6358ba8666ba409ee51b59d5;hp=f56a70b511f02a8ecc813ce5f8d3c06bed471c5c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index f56a70b..d7d07bc 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,27 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 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.
*
* 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.*;
-
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.Format;
-import jalview.datamodel.*;
+import jalview.util.QuickSort;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
/**
* Takes in a vector or array of sequences and column start and column end and
@@ -34,6 +41,8 @@ import jalview.datamodel.*;
*/
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";
@@ -59,11 +68,15 @@ 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;
@@ -84,16 +97,18 @@ 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();
@@ -101,9 +116,11 @@ 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
{
@@ -114,7 +131,7 @@ public class StructureFrequency
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
@@ -123,7 +140,9 @@ public class StructureFrequency
}
else
{
+
bpEnd = findPair(rna, i);
+
if (bpEnd > -1)
{
for (j = 0; j < jSize; j++) // foreach row
@@ -135,28 +154,39 @@ 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++;
@@ -164,15 +194,21 @@ public class StructureFrequency
// UPDATE this for new values
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(PAIRPROFILE, pairs);
}
-
- count = values['('];
-
+ if (wooble == true)
+ {
+ count = values['('];
+ }
+ if (wooble == false)
+ {
+ count = values['['];
+ }
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
@@ -188,11 +224,20 @@ 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[][]
@@ -209,6 +254,7 @@ public class StructureFrequency
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
@@ -309,18 +355,19 @@ 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;
@@ -374,7 +421,7 @@ public class StructureFrequency
* ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; } }
* else {
*/
- 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++)
@@ -387,17 +434,22 @@ public class StructureFrequency
x++;
}
}
- jalview.util.QuickSort.sort(vl, ca);
+ QuickSort.sortFloat(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--)
{
if (vl[c] > 0)
{
- 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) + "%";
+ tval = (vl[c] * 100f / divisor);
+ mouseOver += ((p == 0) ? "" : "; ") + (char) ca[c][0]
+ + (char) ca[c][1] + " " + fmt.formDouble(tval)
+ + "%";
p++;
}
@@ -407,7 +459,7 @@ public class StructureFrequency
}
else
{
- mouseOver += (fmt.form(value) + "%");
+ mouseOver += (fmt.formDouble(value) + "%");
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
@@ -423,16 +475,19 @@ public class StructureFrequency
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
- int[] rtnval = new int[74]; // 2*(5*5)+2
+ 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;
+ }
// TODO fix the object length, also do it in completeConsensus
- Object[] ca = new Object[625];
+ // 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++)
@@ -445,23 +500,30 @@ public class StructureFrequency
x++;
}
}
- jalview.util.QuickSort.sort(vl, ca);
+ QuickSort.sortFloat(vl, ca);
- rtnval[0] = 2;
+ 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[rtnval[0]++] = ((int[]) ca[c])[0];
- rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
- rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0]);
- rtnval[1] += rtnval[rtnval[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[])