X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FPfamFile.java;h=6b9dc3f6a53836eb4573858bd51115744436b138;hb=f63986510999f17f5fa7bf7af09c13cd888adf4e;hp=d0ffbc9a0eb28d3bbdea5d3b6e8e7afef1024b09;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index d0ffbc9..6b9dc3f 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,192 +1,191 @@
-/*
-* 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 PfamFile extends AlignFile {
-
- Vector ids;
-
- public PfamFile()
- {}
-
- public PfamFile(String inStr) {
- super(inStr);
- }
-
- public void initData() {
- super.initData();
- ids = new Vector();
- }
-
- public PfamFile(String inFile, String type) throws IOException {
- super(inFile,type);
- }
-
- public void parse() throws IOException{
- int i = 0;
- String line;
-
-
- Hashtable seqhash = new Hashtable();
- Vector headers = new Vector();
-
-
- while ((line = nextLine()) != null)
- {
-
- if (line.indexOf(" ") != 0)
- {
- if (line.indexOf("#") != 0)
- {
-
- StringTokenizer str = new StringTokenizer(line," ");
- String id = "";
-
- if (str.hasMoreTokens())
- {
- id = str.nextToken();
-
- 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());
- }
- }
- }
- }
-
- this.noSeqs = headers.size();
- if(noSeqs<1)
- throw new IOException("No sequences found (PFAM input)");
-
- 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();
-
- String head = headers.elementAt(i).toString();
- int start = 1;
- int 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
- {
- start = -1;
- end = -1;
- }
- } else
- ids.addElement(headers.elementAt(i));
-
- }
- else
- ids.addElement(headers.elementAt(i));
-
-
- Sequence newSeq = null;
- if (start != -1 && end != -1)
- {
- newSeq = new Sequence(ids.elementAt(i).toString(),
- seqhash.get(headers.elementAt(i).toString()).toString(),start,end);
- seqs.addElement(newSeq);
- }
- else
- {
- newSeq = new Sequence(ids.elementAt(i).toString(),
- seqhash.get(headers.elementAt(i).toString()).toString(),1,
- seqhash.get(headers.elementAt(i).toString()).toString().length());
- seqs.addElement(newSeq);
- }
-
- if(!isValidProteinSequence(newSeq.getSequence()))
- throw new IOException("Not a valid protein sequence - (PFAM input)");
- }
- else
- System.err.println("PFAM File reader: Can't find sequence for " + headers.elementAt(i));
-
- }
-
- }
-
- public static String print(SequenceI[] s) {
- StringBuffer out = new StringBuffer("");
-
- 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;
- }
-
- 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() ) + " ");
-
- out.append(s[j].getSequence() + "\n");
- j++;
- }
- out.append("\n");
-
- return out.toString();
- }
-
- public String print() {
- return print(getSeqsAsArray());
- }
-}
+/*
+ * 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.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+public class PfamFile extends AlignFile
+{
+
+ public PfamFile()
+ {
+ }
+
+ public PfamFile(String inFile, DataSourceType sourceType)
+ throws IOException
+ {
+ super(inFile, sourceType);
+ }
+
+ public PfamFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ @Override
+ public void initData()
+ {
+ super.initData();
+ }
+
+ @Override
+ public void parse() throws IOException
+ {
+ int i = 0;
+ String line;
+
+ HashMap seqhash = new HashMap();
+ ArrayList headers = new ArrayList();
+ boolean useTabs = false;
+ int spces;
+ while ((line = nextLine()) != null)
+ {
+ if (line.indexOf("#") == 0)
+ {
+ // skip comment lines
+ continue;
+ }
+ // locate first space or (if already checked), tab
+ if (useTabs)
+ {
+ spces = line.indexOf("\t");
+ }
+ else
+ {
+ spces = line.indexOf(" ");
+ // check to see if we ought to split on tabs instead.
+ if (!useTabs && spces == -1)
+ {
+ useTabs = true;
+ spces = line.indexOf("\t");
+ }
+ }
+ if (spces <= 0)
+ {
+ // no sequence data to split on
+ continue;
+ }
+ String id = line.substring(0, spces);
+ StringBuffer tempseq;
+
+ if (seqhash.containsKey(id))
+ {
+ tempseq = seqhash.get(id);
+ }
+ else
+ {
+ tempseq = new StringBuffer();
+ seqhash.put(id, tempseq);
+ }
+
+ if (!(headers.contains(id)))
+ {
+ headers.add(id);
+ }
+ if (spces + 1 < line.length())
+ {
+ tempseq.append(line.substring(spces + 1).trim());
+ }
+ }
+
+ this.noSeqs = headers.size();
+
+ if (noSeqs < 1)
+ {
+ throw new IOException(MessageManager
+ .getString("exception.pfam_no_sequences_found"));
+ }
+
+ for (i = 0; i < headers.size(); i++)
+ {
+ if (seqhash.get(headers.get(i)) != null)
+ {
+ if (maxLength < seqhash.get(headers.get(i)).toString().length())
+ {
+ maxLength = seqhash.get(headers.get(i)).toString().length();
+ }
+
+ Sequence newSeq = parseId(headers.get(i).toString());
+ newSeq.setSequence(
+ seqhash.get(headers.get(i).toString()).toString());
+ seqs.addElement(newSeq);
+ }
+ else
+ {
+ System.err.println("PFAM File reader: Can't find sequence for "
+ + headers.get(i));
+ }
+ }
+ }
+
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
+ {
+ StringBuffer out = new StringBuffer("");
+
+ 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;
+ }
+
+ int j = 0;
+
+ while ((j < s.length) && (s[j] != null))
+ {
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[j], jvsuffix) + " "));
+
+ out.append(s[j].getSequenceAsString());
+ out.append(newline);
+ j++;
+ }
+
+ out.append(newline);
+
+ return out.toString();
+ }
+}