--- /dev/null
+/*
+ * Created on 17-May-2005
+ *
+ * TODO To change the template for this generated file go to
+ * Window - Preferences - Java - Code Style - Code Templates
+ */
+package uk.ac.vamsas.objects.utils;
+
+import java.io.BufferedOutputStream;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.regex.Pattern;
+
+import uk.ac.vamsas.objects.core.*;
+
+/**
+ * @author jimp
+ *
+ * TODO To change the template for this generated type comment go to Window -
+ * Preferences - Java - Code Style - Code Templates
+ */
+public class SeqAln extends uk.ac.vamsas.objects.core.Alignment {
+
+ public static Sequence[] ReadClustalFile(InputStream os) throws Exception {
+ System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
+ Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE);
+ String gapchars = "";
+ char gapchar = '-';
+
+ int i = 0;
+ boolean flag = false;
+
+ Vector headers = new Vector();
+ Hashtable seqhash = new Hashtable();
+ Sequence[] seqs = null;
+ int noSeqs = 0;
+ String line;
+
+ try {
+ BufferedReader ins = new BufferedReader(new InputStreamReader(os));
+ while ((line = ins.readLine()) != null) {
+ if (line.indexOf(" ") != 0) {
+ java.util.StringTokenizer str = new StringTokenizer(line, " ");
+ String id = "";
+
+ if (str.hasMoreTokens()) {
+ id = str.nextToken();
+ if (id.equals("CLUSTAL")) {
+ flag = true;
+ } else {
+ if (flag) {
+ StringBuffer tempseq;
+ if (seqhash.containsKey(id)) {
+ tempseq = (StringBuffer) seqhash.get(id);
+ } else {
+ tempseq = new StringBuffer();
+ seqhash.put(id, tempseq);
+ }
+
+ if (!(headers.contains(id))) {
+ headers.addElement(id);
+ }
+
+ tempseq.append(str.nextToken());
+ }
+ }
+ }
+ }
+ }
+
+ } catch (IOException e) {
+ throw (new Exception("Exception parsing clustal file ", e));
+ }
+
+ if (flag) {
+ noSeqs = headers.size();
+
+ // Add sequences to the hash
+ seqs = new Sequence[headers.size()];
+ for (i = 0; i < headers.size(); i++) {
+ if (seqhash.get(headers.elementAt(i)) != null) {
+ // TODO: develop automatic dictionary typing for sequences
+ Sequence newSeq = Seq.newSequence(headers.elementAt(i).toString(),
+ seqhash.get(headers.elementAt(i).toString()).toString(),
+ SymbolDictionary.STANDARD_AA,0,0);
+
+ seqs[i] = newSeq;
+
+ } else {
+ throw (new Exception("Bizarreness! Can't find sequence for "
+ + headers.elementAt(i)));
+ }
+ }
+ }
+ return seqs;
+ }
+
+ public static void WriteClustalWAlignment(java.io.OutputStream os,
+ Alignment seqAl) throws IOException {
+ System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
+ AlignmentSequence[] s = seqAl.getAlignmentSequence();
+
+ java.io.BufferedWriter out = new BufferedWriter(
+ new java.io.OutputStreamWriter(os));
+
+ out.write("CLUSTAL\n\n");
+
+ int max = 0;
+ int maxid = 0;
+
+ int i = 0;
+
+ while (i < s.length && s[i] != null) {
+ String tmp = s[i].getId();
+
+ if (s[i].getSequence().length() > max) {
+ max = s[i].getSequence().length();
+ }
+ if (tmp.length() > maxid) {
+ maxid = tmp.length();
+ }
+ i++;
+ }
+
+ if (maxid < 15) {
+ maxid = 15;
+ }
+ maxid++;
+ int len = 60;
+ int nochunks = max / len + 1;
+
+ for (i = 0; i < nochunks; i++) {
+ int j = 0;
+ while (j < s.length && s[j] != null) {
+ out.write(new Format("%-" + maxid + "s").form(s[j].getId() + " "));
+ int start = i * len;
+ int end = start + len;
+
+ if (end < s[j].getSequence().length() && start < s[j].getSequence().length()) {
+ out.write(s[j].getSequence().substring(start, end) + "\n");
+ } else {
+ if (start < s[j].getSequence().length()) {
+ out.write(s[j].getSequence().substring(start) + "\n");
+ }
+ }
+ j++;
+ }
+ out.write("\n");
+
+ }
+ }
+ /**
+ * manufacture an alignment/dataset from an array of sequences
+ * @param origin
+ * @param seqs
+ * @return
+ * @throws Exception
+ */
+ public static Alignment make_Alignment(Entry origin,
+ Sequence[] seqs) throws Exception {
+ System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
+ Alignment al = new Alignment();
+ al.setProvenance(ProvenanceStuff.newProvenance(origin));
+
+ Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE);
+ boolean gapsset = false;
+ char gapchar = '-';
+ int seqLength = 0;
+
+ for (int i = 0, nseq = seqs.length; i < nseq; i++) {
+ String seq = seqs[i].getSequence();
+ String gaps = nonGap.matcher(seq).replaceAll("");
+ if (seqLength == 0) {
+ seqLength = seq.length();
+ } else if (seqLength != seq.length())
+ throw (new Exception(i + "th Sequence (>" + seqs[i].getId()
+ + ") is not aligned.\n"));// TODO: move this to assertions part of
+ // Alignment
+
+ // common check for any sequence...
+ if (gaps != null && gaps.length() > 0) {
+ if (!gapsset)
+ gapchar = gaps.charAt(0);
+ for (int c = 0, gc = gaps.length(); c < gc; c++) {
+ if (gapchar != gaps.charAt(c)) {
+ throw (new IOException("Inconsistent gap characters in sequence "
+ + i + ": '" + seq + "'"));
+ }
+ }
+ }
+ AlignmentSequence sq = new AlignmentSequence();
+ // TODO: use as basis of default AlignSequence(Sequence) constructor.
+ sq.setSequence(seq);
+ sq.setName(seqs[i].getId());
+ sq.setRefid(seqs[i].getVorbaId());
+ sq.setStart(seqs[i].getStart());
+ sq.setEnd(seqs[i].getEnd());
+ al.addAlignmentSequence(sq);
+ }
+ al.setGapChar(String.valueOf(gapchar));
+ return al;
+ }
+
+ public static Alignment read_FastaAlignment(InputStream os, Entry entry)
+ throws Exception {
+ Sequence[] seqs;
+ System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
+ try {
+ seqs = SeqSet.read_SeqFasta(os);
+ if (seqs == null)
+ throw (new Exception("Empty alignment stream!\n"));
+ } catch (Exception e) {
+ throw new Exception("Invalid fasta alignment\n", e);
+ }
+
+ return make_Alignment(entry, seqs);
+ }
+
+ public static Alignment read_ClustalAlignment(InputStream os, Entry entry)
+ throws Exception {
+ Sequence[] seqs;
+ try {
+ seqs = SeqAln.ReadClustalFile(os);
+ if (seqs == null)
+ throw (new Exception("Empty alignment stream!\n"));
+ } catch (Exception e) {
+ throw new Exception("Invalid fasta alignment\n", e);
+ }
+ System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
+ return make_Alignment(entry, seqs);
+ }
+}
git://source.jalview.org / vamsas.git / blobdiff