-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.analysis;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import java.applet.Applet;\r
-\r
-import java.awt.*;\r
-\r
-import java.io.*;\r
-\r
-import java.net.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class AAFrequency {\r
- // Takes in a vector of sequences and column start and column end\r
- // and returns a vector of size (end-start+1). Each element of the\r
- // vector contains a hashtable with the keys being residues and\r
- // the values being the count of each residue in that column.\r
- // This class is used extensively in calculating alignment colourschemes\r
- // that depend on the amount of conservation in each alignment column.\r
- public static Vector calculate(Vector sequences, int start, int end) {\r
- Vector result = new Vector();\r
-\r
- for (int i = start; i <= end; i++) {\r
- Hashtable residueHash = new Hashtable();\r
- int maxCount = 0;\r
- String maxResidue = "-";\r
- int nongap = 0;\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- if (sequences.elementAt(j) instanceof Sequence) {\r
- Sequence s = (Sequence) sequences.elementAt(j);\r
-\r
- if (s.getSequence().length() > i) {\r
- String res = s.getSequence().charAt(i) + "";\r
-\r
- if (!jalview.util.Comparison.isGap(res.charAt(0))) {\r
- nongap++;\r
- } else {\r
- res = "-"; // we always use this for gaps in the property vectors\r
- }\r
-\r
- if (residueHash.containsKey(res)) {\r
- int count = ((Integer) residueHash.get(res)).intValue();\r
- count++;\r
-\r
- if (!jalview.util.Comparison.isGap(res.charAt(0)) &&\r
- (count >= maxCount)) {\r
- if (count > maxCount) {\r
- maxResidue = res;\r
- } else if (maxResidue.indexOf(res) == -1) {\r
- maxResidue += res;\r
- }\r
-\r
- maxCount = count;\r
- }\r
-\r
- residueHash.put(res, new Integer(count));\r
- } else {\r
- residueHash.put(res, new Integer(1));\r
- }\r
- } else {\r
- if (residueHash.containsKey("-")) {\r
- int count = ((Integer) residueHash.get("-")).intValue();\r
- count++;\r
- residueHash.put("-", new Integer(count));\r
- } else {\r
- residueHash.put("-", new Integer(1));\r
- }\r
- }\r
- }\r
- }\r
-\r
- residueHash.put("maxCount", new Integer(maxCount));\r
-\r
- if (maxCount < 0) {\r
- System.out.println("asasa " + maxCount);\r
- }\r
-\r
- residueHash.put("maxResidue", maxResidue);\r
- residueHash.put("size", new Integer(sequences.size()));\r
- residueHash.put("nongap", new Integer(nongap));\r
- result.addElement(residueHash);\r
- }\r
-\r
- return result;\r
- }\r
-\r
- public static Vector calculatePID(SequenceI refseq, Vector sequences,\r
- int window, int start, int end) {\r
- Vector result = new Vector();\r
-\r
- boolean init = true;\r
-\r
- Vector prev = null;\r
-\r
- for (int i = start; i <= end; i++) {\r
- Vector values = new Vector();\r
-\r
- result.addElement(values);\r
-\r
- // If start < window/2 then set value to zero.\r
- if ((i < (window / 2)) ||\r
- (i >= (refseq.getSequence().length() - (window / 2)))) {\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
- } else if (init == true) {\r
- init = false;\r
-\r
- int winstart = i - (window / 2);\r
- int winend = i + (window / 2);\r
-\r
- if ((window % 2) != 0) {\r
- winend++;\r
- }\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
-\r
- for (int k = winstart; k <= winend; k++) {\r
- String refchar = refseq.getSequence().substring(k, k + 1);\r
-\r
- if (jalview.util.Comparison.isGap(refchar.charAt(0))) {\r
- refchar = "-";\r
- } else {\r
- for (int j = 0; j < sequences.size(); j++) {\r
- Sequence s = (Sequence) sequences.elementAt(j);\r
-\r
- if (s.getSequence().length() > k) {\r
- String res = s.getSequence().substring(k, k +\r
- 1); // no gapchar test needed\r
-\r
- if (res.equals(refchar)) {\r
- int val = ((Integer) values.elementAt(j)).intValue();\r
- val++;\r
- values.setElementAt(new Integer(val), j);\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- prev = values;\r
- } else {\r
- int winstart = i - (window / 2);\r
- int winend = i + (window / 2);\r
-\r
- if ((window % 2) != 0) {\r
- winend++;\r
- }\r
-\r
- // We need to take the previous set of values\r
- // subtract the pid at winstart-1\r
- // and add the pid at winend;\r
- String pre_refchar = refseq.getSequence().substring(winstart -\r
- 1, winstart);\r
- String pos_refchar = "-";\r
-\r
- if (refseq.getSequence().length() > winend) {\r
- pos_refchar = refseq.getSequence().substring(winend,\r
- winend + 1);\r
- }\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- // First copy the pid value from i-1\r
- int val = ((Integer) prev.elementAt(j)).intValue();\r
-\r
- Sequence s = (Sequence) sequences.elementAt(j);\r
-\r
- String pre_char = s.getSequence().substring(winstart - 1,\r
- winstart);\r
-\r
- String pos_char = "-";\r
-\r
- if (s.getSequence().length() > winend) {\r
- pos_char = s.getSequence().substring(winend, winend +\r
- 1);\r
- }\r
-\r
- // Now substract 1 if the chars at winstart-1 match\r
- if ((jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false) &&\r
- pre_char.equals(pre_refchar)) {\r
- val--;\r
- }\r
-\r
- if ((jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false) &&\r
- pos_char.equals(pos_refchar)) {\r
- val++;\r
- }\r
-\r
- values.addElement(new Integer(val));\r
- }\r
-\r
- prev = values;\r
- }\r
- }\r
-\r
- return result;\r
- }\r
-\r
- public static Hashtable findBlocks(Vector seqs, int start, int end,\r
- Vector exc) {\r
- // start and end are in real (not relative coords);\r
- // The coords in the hashtable that is returned are in relative coords\r
- // i.e. start from 0\r
- Hashtable blocks = new Hashtable();\r
-\r
- boolean prev = false;\r
- int bstart = -1;\r
-\r
- for (int i = start; i <= end; i++) {\r
- SequenceI seq = (SequenceI) seqs.elementAt(0);\r
-\r
- char c = seq.getCharAt(i);\r
-\r
- boolean found = true;\r
-\r
- int j = 1;\r
-\r
- while ((j < seqs.size()) && (found == true)) {\r
- SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
-\r
- if (!exc.contains(jseq)) {\r
- char cc = jseq.getCharAt(i);\r
-\r
- if (cc != c) {\r
- found = false;\r
- }\r
- }\r
-\r
- j++;\r
- }\r
-\r
- if ((prev == false) && (found == true)) {\r
- bstart = i;\r
- } else if ((prev == true) && (found == false) && (bstart != -1)) {\r
- int blockstart = bstart - start;\r
- int blocklen = i - bstart;\r
-\r
- //System.out.println("Start len " + blockstart + " " + blocklen);\r
- for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {\r
- blocks.put(new Integer(jj), new Integer(blocklen));\r
- }\r
-\r
- bstart = -1;\r
- }\r
-\r
- prev = found;\r
- }\r
-\r
- if (bstart != -1) {\r
- int blockstart = bstart - start;\r
- int blocklen = end - bstart;\r
-\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
- for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {\r
- blocks.put(new Integer(blockstart), new Integer(blocklen));\r
- }\r
- }\r
-\r
- return blocks;\r
- }\r
-\r
- public static Hashtable findKmerCount(SequenceI seq, int start, int end,\r
- int window, int step, Vector kmers) {\r
- int tmpstart = start;\r
- Hashtable vals = new Hashtable();\r
-\r
- while (tmpstart <= end) {\r
- String tmpstr = seq.getSequence().substring(tmpstart -\r
- (window / 2), tmpstart + (window / 2));\r
-\r
- int count = 0;\r
-\r
- //System.out.println("Str " + tmpstr);\r
- for (int ii = 0; ii < kmers.size(); ii++) {\r
- String kmer = ((SequenceI) kmers.elementAt(ii)).getSequence();\r
-\r
- int i = -1;\r
-\r
- while (tmpstr.indexOf(kmer, i) != -1) {\r
- i = tmpstr.indexOf(kmer, i);\r
-\r
- i++;\r
- count++;\r
- }\r
-\r
- ii++;\r
- }\r
-\r
- vals.put(new Integer(tmpstart), new Integer(count));\r
- tmpstart += step;\r
- }\r
-\r
- return vals;\r
- }\r
-\r
- public static Hashtable findBlockStarts(Vector seqs, int start, int end,\r
- Vector exc) {\r
- // start and end are in real (not relative coords);\r
- // The coords in the hashtable that is returned are in relative coords\r
- // i.e. start from 0\r
- Hashtable blocks = new Hashtable();\r
-\r
- boolean prev = false;\r
- int bstart = -1;\r
-\r
- for (int i = start; i <= end; i++) {\r
- SequenceI seq = (SequenceI) seqs.elementAt(0);\r
-\r
- char c = seq.getCharAt(i);\r
-\r
- boolean found = true;\r
-\r
- int j = 1;\r
-\r
- while ((j < seqs.size()) && (found == true)) {\r
- SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
-\r
- if (!exc.contains(jseq)) {\r
- char cc = jseq.getCharAt(i);\r
-\r
- if (cc != c) {\r
- found = false;\r
- }\r
- }\r
-\r
- j++;\r
- }\r
-\r
- if ((prev == false) && (found == true)) {\r
- bstart = i;\r
- } else if ((prev == true) && (found == false) && (bstart != -1)) {\r
- int blockstart = bstart - start;\r
- int blocklen = i - bstart;\r
-\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart), new Integer(blocklen));\r
-\r
- // }\r
- bstart = -1;\r
- }\r
-\r
- prev = found;\r
- }\r
-\r
- if (bstart != -1) {\r
- int blockstart = bstart - start;\r
- int blocklen = end - bstart;\r
-\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart), new Integer(blocklen));\r
-\r
- // }\r
- }\r
-\r
- return blocks;\r
- }\r
-}\r
+/*
+ * 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
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.util.Format;
+import jalview.datamodel.*;
+
+/**
+ * Takes in a vector or array of sequences and column start and column end and
+ * 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 $Revision$
+ */
+public class AAFrequency
+{
+ // No need to store 1000s of strings which are not
+ // visible to the user.
+ public static final String MAXCOUNT = "C";
+
+ public static final String MAXRESIDUE = "R";
+
+ public static final String PID_GAPS = "G";
+
+ public static final String PID_NOGAPS = "N";
+
+ public static final String PROFILE = "P";
+
+ public static final Hashtable[] calculate(List<SequenceI> list,
+ int start, int end)
+ {
+ return calculate(list, start, end, false);
+ }
+
+ public static final Hashtable[] calculate(List<SequenceI> sequences,
+ int start, int end, boolean profile)
+ {
+ SequenceI[] seqs = new SequenceI[sequences.size()];
+ int width = 0;
+ synchronized (sequences)
+ {
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seqs[i] = sequences.get(i);
+ if (seqs[i].getLength() > width)
+ {
+ width = seqs[i].getLength();
+ }
+ }
+
+ Hashtable[] reply = new Hashtable[width];
+
+ if (end >= width)
+ {
+ end = width;
+ }
+
+ calculate(seqs, start, end, reply, profile);
+ return reply;
+ }
+ }
+
+ public static final void calculate(SequenceI[] sequences, int start,
+ int end, Hashtable[] result)
+ {
+ calculate(sequences, start, end, result, false);
+ }
+
+ public static final void calculate(SequenceI[] sequences, int start,
+ int end, Hashtable[] result, boolean profile)
+ {
+ Hashtable residueHash;
+ int maxCount, nongap, i, j, v, jSize = sequences.length;
+ String maxResidue;
+ char c='-';
+ float percentage;
+
+ int[] values = new int[255];
+
+ char[] seq;
+
+ for (i = start; i < end; i++)
+ {
+ residueHash = new Hashtable();
+ maxCount = 0;
+ maxResidue = "";
+ nongap = 0;
+ values = new int[255];
+
+ for (j = 0; j < jSize; j++)
+ {
+ if (sequences[j] == null)
+ {
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
+ }
+ seq = sequences[j].getSequence();
+ if (seq.length > i)
+ {
+ c = seq[i];
+
+ if (c == '.' || c == ' ')
+ {
+ c = '-';
+ }
+
+ if (c == '-')
+ {
+ values['-']++;
+ continue;
+ }
+ else if ('a' <= c && c <= 'z')
+ {
+ c -= 32; // ('a' - 'A');
+ }
+
+ nongap++;
+ values[c]++;
+
+ }
+ else
+ {
+ values['-']++;
+ }
+ }
+ if (jSize==1)
+ {
+ maxResidue = String.valueOf(c);
+ maxCount=1;
+ } else {for (v = 'A'; v < 'Z'; v++)
+ {
+ if (values[v] < 2 || values[v] < maxCount)
+ {
+ continue;
+ }
+
+ if (values[v] > maxCount)
+ {
+ maxResidue = String.valueOf((char) v);
+ }
+ else if (values[v] == maxCount)
+ {
+ maxResidue += String.valueOf((char) v);
+ }
+ maxCount = values[v];
+ }
+ }
+ if (maxResidue.length() == 0)
+ {
+ maxResidue = "-";
+ }
+ if (profile)
+ {
+ residueHash.put(PROFILE, new int[][]
+ { values, new int[]
+ { jSize, nongap } });
+ }
+ residueHash.put(MAXCOUNT, new Integer(maxCount));
+ residueHash.put(MAXRESIDUE, maxResidue);
+
+ percentage = ((float) maxCount * 100) / jSize;
+ residueHash.put(PID_GAPS, new Float(percentage));
+
+ if (nongap>0) {
+ // calculate for non-gapped too
+ percentage = ((float) maxCount * 100) / nongap;
+ }
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
+ result[i] = residueHash;
+ }
+ }
+
+ /**
+ * Compute all or part of the annotation row from the given consensus
+ * hashtable
+ *
+ * @param consensus
+ * - pre-allocated annotation row
+ * @param hconsensus
+ * @param iStart
+ * @param width
+ * @param ignoreGapsInConsensusCalculation
+ * @param includeAllConsSymbols
+ * @param nseq
+ */
+ public static void completeConsensus(AlignmentAnnotation consensus,
+ Hashtable[] hconsensus, int iStart, int width,
+ boolean ignoreGapsInConsensusCalculation,
+ boolean includeAllConsSymbols, long nseq)
+ {
+ completeConsensus(consensus, hconsensus, iStart, width,
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
+ // char[]
+ // { 'A', 'C', 'G', 'T', 'U' });
+ }
+
+ public static void completeConsensus(AlignmentAnnotation consensus,
+ Hashtable[] hconsensus, int iStart, int width,
+ boolean ignoreGapsInConsensusCalculation,
+ boolean includeAllConsSymbols, char[] alphabet, long nseq)
+ {
+ float tval, value;
+ if (consensus == null || consensus.annotations == null
+ || consensus.annotations.length < width)
+ {
+ // called with a bad alignment annotation row - wait for it to be
+ // initialised properly
+ return;
+ }
+ String fmtstr="%3.1f";
+ int precision=0;
+ while (nseq>=10) {
+ precision++;
+ nseq/=10;
+ }
+ final Format fmt;
+ if (precision>1)
+ {
+ //if (precision>2)
+ {
+ fmtstr = "%"+(2+precision)+"."+(precision)+"f";
+ }
+ fmt = new Format(fmtstr);
+ } else {
+ fmt = null;
+ }
+ for (int i = iStart; i < width; i++)
+ {
+ Hashtable hci;
+ if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
+ {
+ // happens if sequences calculated over were shorter than alignment
+ // width
+ consensus.annotations[i] = null;
+ continue;
+ }
+ value = 0;
+ Float fv;
+ if (ignoreGapsInConsensusCalculation)
+ {
+ fv = (Float) hci.get(AAFrequency.PID_NOGAPS);
+ }
+ else
+ {
+ fv = (Float) hci.get(AAFrequency.PID_GAPS);
+ }
+ if (fv == null)
+ {
+ consensus.annotations[i] = null;
+ // data has changed below us .. give up and
+ continue;
+ }
+ value = fv.floatValue();
+ String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " ";
+ if (maxRes.length() > 1)
+ {
+ mouseOver = "[" + maxRes + "] ";
+ maxRes = "+";
+ }
+ int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
+ if (profile != null && includeAllConsSymbols)
+ {
+ mouseOver = "";
+ if (alphabet != null)
+ {
+ for (int c = 0; c < alphabet.length; c++)
+ {
+ tval = profile[0][alphabet[c]] * 100f
+ / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
+ + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
+ }
+ }
+ else
+ {
+ Object[] ca = new Object[profile[0].length];
+ float[] vl = new float[profile[0].length];
+ for (int c = 0; c < ca.length; c++)
+ {
+ ca[c] = new char[]
+ { (char) c };
+ vl[c] = profile[0][c];
+ }
+ ;
+ jalview.util.QuickSort.sort(vl, ca);
+ for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ {
+ if (((char[]) ca[c])[0] != '-')
+ {
+ tval = profile[0][((char[]) ca[c])[0]]
+ * 100f
+ / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
+ + " " + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
+ p++;
+
+ }
+ }
+
+ }
+ }
+ else
+ {
+ mouseOver += ((fmt!=null) ? fmt.form(value) : ((int) value)) + "%";
+ }
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+ value);
+ }
+ }
+
+ /**
+ * get the sorted profile for the given position of the consensus
+ *
+ * @param hconsensus
+ * @return
+ */
+ public static int[] extractProfile(Hashtable hconsensus,
+ boolean ignoreGapsInConsensusCalculation)
+ {
+ int[] rtnval = new int[64];
+ int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
+ if (profile == null)
+ return null;
+ Object[] ca = new Object[profile[0].length];
+ float[] vl = new float[profile[0].length];
+ for (int c = 0; c < ca.length; c++)
+ {
+ ca[c] = new char[]
+ { (char) c };
+ vl[c] = profile[0][c];
+ }
+ ;
+ jalview.util.QuickSort.sort(vl, ca);
+ rtnval[0] = 2;
+ rtnval[1] = 0;
+ for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ {
+ if (((char[]) ca[c])[0] != '-')
+ {
+ rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
+ rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0]);
+ rtnval[1] += rtnval[rtnval[0]++];
+ }
+ }
+ return rtnval;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff