X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=c5581867c48d1934c4c4b8cfaede90e62de08147;hb=refs%2Fheads%2Fpatch%2FJAL-1236_customClustalHeader;hp=d62d185d9afda45c67c1e5efa4b0f419490de4fa;hpb=3a993bbe274824870c78bd7695c42fa93908cb30;p=jalview.git
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index d62d185..c558186 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,75 +1,103 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * 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.
- *
- * 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 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.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
-import jalview.util.*;
+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 class ClustalFile extends AlignFile
{
public ClustalFile()
{
+ _initHeader();
}
- public ClustalFile(String inFile, String type)
- throws IOException
+ public ClustalFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
+ _initHeader();
}
+
public ClustalFile(FileParse source) throws IOException
{
super(source);
+ _initHeader();
+ }
+
+ private void _initHeader()
+ {
+ try {
+ clustalHeader = jalview.bin.Cache.getDefault("CLUSTAL_HEADER","CLUSTAL");
+ } catch (Error e) {};
+
}
+
+ @Override
public void initData()
{
super.initData();
}
- public void parse()
- throws IOException
+ @Override
+ public void parse() throws IOException
{
int i = 0;
boolean flag = false;
-
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
+ 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)
+ while ((line = nextLine()) != null)
{
- if (line.indexOf(" ") != 0)
+ if (line.length() == 0)
+ {
+ top = true;
+ }
+ boolean isConservation = line.startsWith(SPACE)
+ || line.startsWith(TAB);
+ if (!isConservation)
{
- str = new StringTokenizer(line, " ");
+ str = new StringTokenizer(line);
if (str.hasMoreTokens())
{
id = str.nextToken();
-
+ // TODO: JAL-1236 other tokens may be indicative of a header for Clustal format
if (id.equalsIgnoreCase("CLUSTAL"))
{
flag = true;
@@ -80,7 +108,7 @@ public class ClustalFile
{
if (seqhash.containsKey(id))
{
- tempseq = (StringBuffer) seqhash.get(id);
+ tempseq = seqhash.get(id);
}
else
{
@@ -88,7 +116,7 @@ public class ClustalFile
seqhash.put(id, tempseq);
}
- if (! (headers.contains(id)))
+ if (!(headers.contains(id)))
{
headers.addElement(id);
}
@@ -97,6 +125,7 @@ public class ClustalFile
{
tempseq.append(str.nextToken());
}
+ top = false;
}
}
}
@@ -105,9 +134,22 @@ public class ClustalFile
flag = true;
}
}
+ else
+ {
+ if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
+ {
+ if (top)
+ {
+ pssecstr.append(line.trim());
+ }
+ else
+ {
+ consstr.append(line.trim());
+ }
+ }
+ }
}
- }
- catch (IOException e)
+ } catch (IOException e)
{
System.err.println("Exception parsing clustal file " + e);
e.printStackTrace();
@@ -117,56 +159,74 @@ public class ClustalFile
{
this.noSeqs = headers.size();
- //Add sequences to the hash
+ // 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())
+ .length())
{
maxLength = seqhash.get(headers.elementAt(i)).toString()
- .length();
+ .length();
}
Sequence newSeq = parseId(headers.elementAt(i).toString());
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
- 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));
+ 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);
}
}
}
}
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- public String print(SequenceI[] s)
+ /**
+ * clustal header - customise if needed
+ */
+ public String clustalHeader = "CLUSTAL";
+
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
- StringBuffer out = new StringBuffer("CLUSTAL\n\n");
+ StringBuffer out = new StringBuffer(clustalHeader + newline + newline);
int max = 0;
int maxid = 0;
int i = 0;
- while ( (i < s.length) && (s[i] != null))
+ 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)
{
@@ -184,37 +244,38 @@ public class ClustalFile
maxid++;
int len = 60;
- int nochunks = (max / len) + 1;
+ 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))
+ 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) + " "));
- int start = i * len;
- int end = start + len;
+ int chunkStart = i * len;
+ int chunkEnd = chunkStart + len;
- if ( (end < s[j].getSequence().length) &&
- (start < s[j].getSequence().length))
+ int length = s[j].getLength();
+ if ((chunkEnd < length) && (chunkStart < length))
{
- out.append(s[j].getSequenceAsString(start, end));
+ out.append(s[j].getSequenceAsString(chunkStart, chunkEnd));
}
else
{
- if (start < s[j].getSequence().length)
+ if (chunkStart < length)
{
- out.append(s[j].getSequenceAsString().substring(start));
+ out.append(s[j].getSequenceAsString().substring(chunkStart));
}
}
- out.append("\n");
+ out.append(newline);
j++;
}
- out.append("\n");
+ out.append(newline);
}
return out.toString();