X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=6b9dc3f6a53836eb4573858bd51115744436b138;hb=08c7bee16c16563cc7cec7ea4d336b3e0c4c937a;hp=223e7a468d0a924bc6d16b11e64825bf09df720f;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 223e7a4..6b9dc3f 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,28 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+import jalview.util.MessageManager;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
public class PfamFile extends AlignFile
{
@@ -31,9 +36,10 @@ public class PfamFile extends AlignFile
{
}
- public PfamFile(String inFile, String type) throws IOException
+ public PfamFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public PfamFile(FileParse source) throws IOException
@@ -41,86 +47,104 @@ public class PfamFile extends AlignFile
super(source);
}
+ @Override
public void initData()
{
super.initData();
}
+ @Override
public void parse() throws IOException
{
int i = 0;
String line;
- Hashtable seqhash = new Hashtable();
- Vector headers = new Vector();
-
+ HashMap seqhash = new HashMap();
+ ArrayList headers = new ArrayList();
+ boolean useTabs = false;
+ int spces;
while ((line = nextLine()) != null)
{
- if (line.indexOf(" ") != 0)
+ if (line.indexOf("#") == 0)
{
- 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)
{
- 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());
- }
+ 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("No sequences found (PFAM input)");
+ throw new IOException(MessageManager
+ .getString("exception.pfam_no_sequences_found"));
}
for (i = 0; i < headers.size(); i++)
{
- if (seqhash.get(headers.elementAt(i)) != null)
+ if (seqhash.get(headers.get(i)) != null)
{
- if (maxLength < seqhash.get(headers.elementAt(i)).toString()
- .length())
+ if (maxLength < seqhash.get(headers.get(i)).toString().length())
{
- maxLength = seqhash.get(headers.elementAt(i)).toString().length();
+ maxLength = seqhash.get(headers.get(i)).toString().length();
}
- Sequence newSeq = parseId(headers.elementAt(i).toString());
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
- .toString());
+ 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.elementAt(i));
+ + headers.get(i));
}
}
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("");
@@ -131,12 +155,9 @@ public class PfamFile extends AlignFile
while ((i < s.length) && (s[i] != null))
{
- String tmp = printId(s[i]);
+ String tmp = printId(s[i], jvsuffix);
- if (s[i].getSequence().length > max)
- {
- max = s[i].getSequence().length;
- }
+ max = Math.max(max, s[i].getLength());
if (tmp.length() > maxid)
{
@@ -155,19 +176,16 @@ public class PfamFile extends AlignFile
while ((j < s.length) && (s[j] != null))
{
- out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[j], jvsuffix) + " "));
- out.append(s[j].getSequenceAsString() + "\n");
+ out.append(s[j].getSequenceAsString());
+ out.append(newline);
j++;
}
- out.append("\n");
+ out.append(newline);
return out.toString();
}
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
}