X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FClustalFile.java;h=afb2009e7ca241d7e6e870cb0bdddc1bfcf478fe;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=9b565266332efe7307cc58b653db083c35279b15;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 9b56526..afb2009 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,198 +1,268 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.io;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-public class ClustalFile extends AlignFile {
-
- Vector ids;
-
- public ClustalFile()
- {}
-
- public ClustalFile(String inStr) {
- super(inStr);
- }
-
-
- public void initData() {
- super.initData();
- ids = new Vector();
- }
-
- public ClustalFile(String inFile, String type) throws IOException {
- super(inFile,type);
- }
-
- public void parse() {
- int i = 0;
- boolean flag = false;
-
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
-
- String line;
-
- try {
- while ((line = nextLine()) != null) {
- if (line.indexOf(" ") != 0) {
- 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);
- }
-
- if(str.hasMoreTokens())
- tempseq.append(str.nextToken());
- }
- }
- }
- }
- }
- } catch (IOException e) {
- System.err.println("Exception parsing clustal file " + e);
- e.printStackTrace();
- }
-
- if (flag) {
- this.noSeqs = headers.size();
-
- //Add sequences to the hash
- for (i = 0; i < headers.size(); i++ ) {
- int start = -1;
- int end = -1;
-
- if ( seqhash.get(headers.elementAt(i)) != null) {
- if (maxLength < seqhash.get(headers.elementAt(i)).toString().length() ) {
- maxLength = seqhash.get(headers.elementAt(i)).toString().length();
- }
- String head = headers.elementAt(i).toString();
- start = 1;
- end = seqhash.get(headers.elementAt(i)).toString().length();
-
- if (head.indexOf("/") > 0 ) {
- StringTokenizer st = new StringTokenizer(head,"/");
- if (st.countTokens() == 2) {
-
- ids.addElement(st.nextToken());
-
- String tmp = st.nextToken();
- st = new StringTokenizer(tmp,"-");
- if (st.countTokens() == 2) {
- start = Integer.valueOf(st.nextToken()).intValue();
- end = Integer.valueOf(st.nextToken()).intValue();
- }
- } else {
- ids.addElement(headers.elementAt(i));
- }
- } else {
- ids.addElement(headers.elementAt(i));
-
- }
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
- seqhash.get(headers.elementAt(i).toString()).toString(),start,end);
-
- seqs.addElement(newSeq);
-
- } else {
- System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i));
- }
- }
- }
-
- }
-
- public String print() {
- return print(getSeqsAsArray());
- }
- public static String print(SequenceI[] s) {
-
- StringBuffer out = new StringBuffer("CLUSTAL\n\n");
-
- int max = 0;
- int maxid = 0;
-
- int i = 0;
-
- while (i < s.length && s[i] != null) {
- String tmp = s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd();
-
- 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.append( new Format("%-" + maxid + "s").form(s[j].getName() + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
- int start = i*len;
- int end = start + len;
-
- if (end < s[j].getSequence().length() && start < s[j].getSequence().length() )
- out.append(s[j].getSequence().substring(start,end));
- else
- {
- if (start < s[j].getSequence().length())
- out.append(s[j].getSequence().substring(start));
- }
- out.append("\n");
- j++;
- }
- out.append("\n");
-
- }
-
- return out.toString();
- }
-
-
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+public class ClustalFile extends AlignFile
+{
+
+ public ClustalFile()
+ {
+ }
+
+ public ClustalFile(String inFile, DataSourceType sourceType)
+ throws IOException
+ {
+ super(inFile, sourceType);
+ }
+
+ public ClustalFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ @Override
+ public void initData()
+ {
+ super.initData();
+ }
+
+ @Override
+ public void parse() throws IOException
+ {
+ int i = 0;
+ boolean flag = false;
+ boolean top = false;
+ StringBuffer pssecstr = new StringBuffer();
+ StringBuffer consstr = new StringBuffer();
+ Vector headers = new Vector<>();
+ Map seqhash = new HashMap<>();
+ StringBuffer tempseq;
+ String line, id;
+ StringTokenizer str;
+
+ try
+ {
+ while ((line = nextLine()) != null)
+ {
+ if (line.length() == 0)
+ {
+ top = true;
+ }
+ boolean isConservation = line.startsWith(SPACE)
+ || line.startsWith(TAB);
+ if (!isConservation)
+ {
+ str = new StringTokenizer(line);
+
+ if (str.hasMoreTokens())
+ {
+ id = str.nextToken();
+
+ if (id.equalsIgnoreCase("CLUSTAL"))
+ {
+ flag = true;
+ }
+ else
+ {
+ if (flag)
+ {
+ if (seqhash.containsKey(id))
+ {
+ tempseq = seqhash.get(id);
+ }
+ else
+ {
+ tempseq = new StringBuffer();
+ seqhash.put(id, tempseq);
+ }
+
+ if (!(headers.contains(id)))
+ {
+ headers.addElement(id);
+ }
+
+ if (str.hasMoreTokens())
+ {
+ tempseq.append(str.nextToken());
+ }
+ top = false;
+ }
+ }
+ }
+ else
+ {
+ flag = true;
+ }
+ }
+ else
+ {
+ if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
+ {
+ if (top)
+ {
+ pssecstr.append(line.trim());
+ }
+ else
+ {
+ consstr.append(line.trim());
+ }
+ }
+ }
+ }
+ } catch (IOException e)
+ {
+ System.err.println("Exception parsing clustal file " + e);
+ e.printStackTrace();
+ }
+
+ if (flag)
+ {
+ this.noSeqs = headers.size();
+
+ // Add sequences to the hash
+ for (i = 0; i < headers.size(); i++)
+ {
+ if (seqhash.get(headers.elementAt(i)) != null)
+ {
+ if (maxLength < seqhash.get(headers.elementAt(i)).toString()
+ .length())
+ {
+ maxLength = seqhash.get(headers.elementAt(i)).toString()
+ .length();
+ }
+
+ Sequence newSeq = parseId(headers.elementAt(i).toString());
+ newSeq.setSequence(
+ seqhash.get(headers.elementAt(i).toString()).toString());
+
+ seqs.addElement(newSeq);
+ }
+ else
+ {
+ System.err.println("Clustal File Reader: Can't find sequence for "
+ + headers.elementAt(i));
+ }
+ }
+ AlignmentAnnotation lastssa = null;
+ if (pssecstr.length() == maxLength)
+ {
+ Vector ss = new Vector<>();
+ AlignmentAnnotation ssa = lastssa = StockholmFile
+ .parseAnnotationRow(ss, "secondary structure",
+ pssecstr.toString());
+ ssa.label = "Secondary Structure";
+ annotations.addElement(ssa);
+ }
+ if (consstr.length() == maxLength)
+ {
+ Vector ss = new Vector<>();
+ AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
+ "secondary structure", consstr.toString());
+ ssa.label = "Consensus Secondary Structure";
+ if (lastssa == null || !lastssa.getRNAStruc()
+ .equals(ssa.getRNAStruc().replace('-', '.')))
+ {
+ annotations.addElement(ssa);
+ }
+ }
+ }
+ }
+
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
+ {
+ StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
+
+ int max = 0;
+ int maxid = 0;
+
+ int i = 0;
+
+ while ((i < s.length) && (s[i] != null))
+ {
+ String tmp = printId(s[i], jvsuffix);
+
+ max = Math.max(max, s[i].getLength());
+
+ if (tmp.length() > maxid)
+ {
+ maxid = tmp.length();
+ }
+
+ i++;
+ }
+
+ if (maxid < 15)
+ {
+ maxid = 15;
+ }
+
+ maxid++;
+
+ int len = 60;
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
+
+ for (i = 0; i < nochunks; i++)
+ {
+ int j = 0;
+
+ while ((j < s.length) && (s[j] != null))
+ {
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[j], jvsuffix) + " "));
+
+ int chunkStart = i * len;
+ int chunkEnd = chunkStart + len;
+
+ int length = s[j].getLength();
+ if ((chunkEnd < length) && (chunkStart < length))
+ {
+ out.append(s[j].getSequenceAsString(chunkStart, chunkEnd));
+ }
+ else
+ {
+ if (chunkStart < length)
+ {
+ out.append(s[j].getSequenceAsString().substring(chunkStart));
+ }
+ }
+
+ out.append(newline);
+ j++;
+ }
+
+ out.append(newline);
+ }
+
+ return out.toString();
+ }
+}