git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-845 tweaks and bug fixes for split frame view
[jalview.git]
/
src
/
jalview
/
analysis
/
StructureFrequency.java
diff --git
a/src/jalview/analysis/StructureFrequency.java
b/src/jalview/analysis/StructureFrequency.java
index
0c9f830
..
5cf4e30
100644
(file)
--- a/
src/jalview/analysis/StructureFrequency.java
+++ b/
src/jalview/analysis/StructureFrequency.java
@@
-1,26
+1,33
@@
/*
/*
- * 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 ($$Version-Rel$$)
+ * 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
*
* 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.
*
* 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;
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 java.util.ArrayList;
+import java.util.Hashtable;
/**
* Takes in a vector or array of sequences and column start and column end and
/**
* Takes in a vector or array of sequences and column start and column end and
@@
-33,6
+40,8
@@
import jalview.datamodel.*;
*/
public class StructureFrequency
{
*/
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";
// No need to store 1000s of strings which are not
// visible to the user.
public static final String MAXCOUNT = "C";
@@
-58,11
+67,15
@@
public class StructureFrequency
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
+
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
+
{
{
+
return pairs[i].getEnd();
return pairs[i].getEnd();
+
}
}
return -1;
}
}
return -1;
@@
-83,16
+96,18
@@
public class StructureFrequency
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
+
Hashtable residueHash;
String maxResidue;
Hashtable residueHash;
String maxResidue;
- char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ char[] struc = rnaStruc.getRNAStruc().toCharArray();
+
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
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;
int[] values;
int[][] pairs;
float percentage;
-
+ boolean wooble = true;
for (i = start; i < end; i++) // foreach column
{
residueHash = new Hashtable();
for (i = start; i < end; i++) // foreach column
{
residueHash = new Hashtable();
@@
-100,9
+115,11
@@
public class StructureFrequency
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
+ // System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
if (i < struc.length)
{
s = struc[i];
+
}
else
{
}
else
{
@@
-113,7
+130,7
@@
public class StructureFrequency
s = '-';
}
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
{
if (s == '-')
{
@@
-122,19
+139,21
@@
public class StructureFrequency
}
else
{
}
else
{
+
bpEnd = findPair(rna, i);
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 == ' ')
// standard representation for gaps in sequence and structure
if (c == '.' || c == ' ')
@@
-148,34
+167,51
@@
public class StructureFrequency
continue;
}
cEnd = sequences[j].getCharAt(bpEnd);
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)
{
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]++;
}
pairs[c][cEnd]++;
- maxResidue = "(";
}
}
}
}
- }
// nonGap++;
}
// UPDATE this for new values
if (profile)
{
// nonGap++;
}
// 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);
}
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);
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;
residueHash.put(PID_GAPS, new Float(percentage));
// percentage = ((float) count * 100) / (float) nongap;
@@
-187,11
+223,20
@@
public class StructureFrequency
if (bpEnd > 0)
{
values[')'] = values['('];
if (bpEnd > 0)
{
values[')'] = values['('];
+ values[']'] = values['['];
values['('] = 0;
values['('] = 0;
-
+ values['['] = 0;
residueHash = new Hashtable();
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[][]
if (profile)
{
residueHash.put(PROFILE, new int[][]
@@
-204,10
+249,11
@@
public class StructureFrequency
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
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;
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
}
}
}
@@
-298,7
+344,7
@@
public class StructureFrequency
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
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
{
float tval, value;
if (consensus == null || consensus.annotations == null
@@
-308,9
+354,23
@@
public class StructureFrequency
// initialised properly
return;
}
// 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++)
{
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
{
// happens if sequences calculated over were shorter than alignment
// width
@@
-318,30
+378,31
@@
public class StructureFrequency
continue;
}
value = 0;
continue;
}
value = 0;
+ Float fv;
if (ignoreGapsInConsensusCalculation)
{
if (ignoreGapsInConsensusCalculation)
{
- value = ((Float) hconsensus[i].get(StructureFrequency.PID_NOGAPS))
- .floatValue();
+ fv = (Float) hci.get(StructureFrequency.PID_NOGAPS);
}
else
{
}
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 = "+";
}
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
if (pairs != null && includeAllConsSymbols) // Just responsible for the
// tooltip
@@
-349,7
+410,9
@@
public class StructureFrequency
{
mouseOver = "";
{
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)
*
* if (alphabet != null) { for (int c = 0; c < alphabet.length; c++) {
* tval = ((float) profile[0][alphabet[c]]) 100f / (float)
@@
-366,7
+429,7
@@
public class StructureFrequency
{
ca[x] = new int[]
{ c, d };
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
x++;
}
}
@@
-377,10
+440,11
@@
public class StructureFrequency
{
if (vl[c] > 0)
{
{
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]
: 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++;
}
p++;
}
@@
-390,7
+454,7
@@
public class StructureFrequency
}
else
{
}
else
{
- mouseOver += ((int) value + "%");
+ mouseOver += (fmt.form(value) + "%");
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
@@
-406,16
+470,19
@@
public class StructureFrequency
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
- int[] rtnval = new int[52]; // 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)
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
if (profile == null)
+ {
return null;
return null;
+ }
// TODO fix the object length, also do it in completeConsensus
// 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++)
float[] vl = new float[625];
int x = 0;
for (int c = 65; c < 90; c++)
@@
-424,27
+491,34
@@
public class StructureFrequency
{
ca[x] = new int[]
{ c, d };
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
jalview.util.QuickSort.sort(vl, ca);
x++;
}
}
jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 2;
+ int valuesCount = 0;
rtnval[1] = 0;
rtnval[1] = 0;
+ int offset = 2;
for (int c = 624; c > 0; c--)
{
if (vl[c] > 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) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ rtnval[offset++] = ca[c][0];
+ rtnval[offset++] = ca[c][1];
+ rtnval[offset] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
: 0]);
- rtnval[1]+=rtnval[rtnval[0]++];
+ 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[])
}
public static void main(String args[])