X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=dc0212e9f255e20f47519d000c1ac4050921eb35;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=1eab77e906dacd7fd702e6fc8d3ca693da55d7c6;hpb=661f9e271e4c0225773971848b7e310a20dbe967;p=jalview.git
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 1eab77e..dc0212e 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,25 +1,28 @@
/*
- * 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.
- *
- * 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
+ * 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.
+ *
+ * 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.util.Format;
import jalview.datamodel.*;
/**
@@ -27,7 +30,7 @@ import jalview.datamodel.*;
* returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
* This class is used extensively in calculating alignment colourschemes that
* depend on the amount of conservation in each alignment column.
- *
+ *
* @author $author$
* @version $Revision$
*/
@@ -49,7 +52,7 @@ public class StructureFrequency
/**
* Returns the 3' position of a base pair
- *
+ *
* @param pairs
* Secondary structure annotation
* @param indice
@@ -58,11 +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;
@@ -71,7 +78,7 @@ public class StructureFrequency
/**
* Method to calculate a 'base pair consensus row', very similar to nucleotide
* consensus but takes into account a given structure
- *
+ *
* @param sequences
* @param start
* @param end
@@ -83,16 +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();
@@ -100,9 +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
{
@@ -113,7 +124,7 @@ public class StructureFrequency
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
@@ -122,19 +133,21 @@ public class StructureFrequency
}
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 == ' ')
@@ -148,16 +161,27 @@ public class StructureFrequency
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
@@ -169,9 +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);
@@ -187,11 +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[][]
@@ -208,13 +246,14 @@ public class StructureFrequency
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
/**
* Method to check if a base-pair is a canonical or a wobble bp
- *
+ *
* @param up
* 5' base
* @param down
@@ -286,7 +325,7 @@ public class StructureFrequency
/**
* Compute all or part of the annotation row from the given consensus
* hashtable
- *
+ *
* @param consensus
* - pre-allocated annotation row
* @param hconsensus
@@ -298,7 +337,7 @@ public class StructureFrequency
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
@@ -308,9 +347,23 @@ public class StructureFrequency
// 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
@@ -318,30 +371,31 @@ public class StructureFrequency
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
@@ -349,8 +403,10 @@ public class StructureFrequency
{
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)
* profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver +=
@@ -380,7 +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] + " " + ((int) tval) + "%";
+ + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval)
+ + "%";
p++;
}
@@ -390,7 +447,7 @@ public class StructureFrequency
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += (fmt.form(value) + "%");
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
@@ -399,7 +456,7 @@ public class StructureFrequency
/**
* get the sorted base-pair profile for the given position of the consensus
- *
+ *
* @param hconsensus
* @return profile of the given column
*/
@@ -440,7 +497,7 @@ public class StructureFrequency
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[1] += rtnval[rtnval[0]++];
}
}