import java.awt.*;
import jalview.datamodel.*;
+import jalview.io.FileParse;
public class PDBfile
extends jalview.io.AlignFile
super(inFile, inType);
}
+ public PDBfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
public String print()
{
return null;
parse();
}
-
+ /**
+ * Attempt to read from the position where some other parsing process left off.
+ * @param source
+ * @throws IOException
+ */
+ public AlignFile(FileParse source) throws IOException
+ {
+ super(source);
+ initData();
+ parse();
+ }
/**
* Return the seqs Vector
*/
{
super(inFile, type);
}
+ public BLCFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
/**
* DOCUMENT ME!
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-\r
-public class ClustalFile\r
- extends AlignFile\r
-{\r
-\r
- public ClustalFile()\r
- {\r
- }\r
-\r
- public ClustalFile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public void initData()\r
- {\r
- super.initData();\r
- }\r
-\r
- public void parse()\r
- throws IOException\r
- {\r
- int i = 0;\r
- boolean flag = false;\r
-\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
- StringBuffer tempseq;\r
- String line, id;\r
- StringTokenizer str;\r
-\r
- try\r
- {\r
- while ( (line = nextLine()) != null)\r
- {\r
- if (line.indexOf(" ") != 0)\r
- {\r
- str = new StringTokenizer(line, " ");\r
-\r
- if (str.hasMoreTokens())\r
- {\r
- id = str.nextToken();\r
-\r
- if (id.equalsIgnoreCase("CLUSTAL"))\r
- {\r
- flag = true;\r
- }\r
- else\r
- {\r
- if (flag)\r
- {\r
- if (seqhash.containsKey(id))\r
- {\r
- tempseq = (StringBuffer) seqhash.get(id);\r
- }\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(id, tempseq);\r
- }\r
-\r
- if (! (headers.contains(id)))\r
- {\r
- headers.addElement(id);\r
- }\r
-\r
- if (str.hasMoreTokens())\r
- {\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- flag = true;\r
- }\r
- }\r
- }\r
- }\r
- catch (IOException e)\r
- {\r
- System.err.println("Exception parsing clustal file " + e);\r
- e.printStackTrace();\r
- }\r
-\r
- if (flag)\r
- {\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++)\r
- {\r
- if (seqhash.get(headers.elementAt(i)) != null)\r
- {\r
- if (maxLength < seqhash.get(headers.elementAt(i)).toString()\r
- .length())\r
- {\r
- maxLength = seqhash.get(headers.elementAt(i)).toString()\r
- .length();\r
- }\r
-\r
- Sequence newSeq = parseId(headers.elementAt(i).toString());\r
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).\r
- toString());\r
-\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- System.err.println(\r
- "Clustal File Reader: Can't find sequence for " +\r
- headers.elementAt(i));\r
- }\r
- }\r
- }\r
- }\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-\r
- public String print(SequenceI[] s)\r
- {\r
- StringBuffer out = new StringBuffer("CLUSTAL\n\n");\r
-\r
- int max = 0;\r
- int maxid = 0;\r
-\r
- int i = 0;\r
-\r
- while ( (i < s.length) && (s[i] != null))\r
- {\r
- String tmp = printId(s[i]);\r
-\r
- if (s[i].getSequence().length > max)\r
- {\r
- max = s[i].getSequence().length;\r
- }\r
-\r
- if (tmp.length() > maxid)\r
- {\r
- maxid = tmp.length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if (maxid < 15)\r
- {\r
- maxid = 15;\r
- }\r
-\r
- maxid++;\r
-\r
- int len = 60;\r
- int nochunks = (max / len) + 1;\r
-\r
- for (i = 0; i < nochunks; i++)\r
- {\r
- int j = 0;\r
-\r
- while ( (j < s.length) && (s[j] != null))\r
- {\r
- out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));\r
-\r
- int start = i * len;\r
- int end = start + len;\r
-\r
- if ( (end < s[j].getSequence().length) &&\r
- (start < s[j].getSequence().length))\r
- {\r
- out.append(s[j].getSequenceAsString(start, end));\r
- }\r
- else\r
- {\r
- if (start < s[j].getSequence().length)\r
- {\r
- out.append(s[j].getSequenceAsString().substring(start));\r
- }\r
- }\r
-\r
- out.append("\n");\r
- j++;\r
- }\r
-\r
- out.append("\n");\r
- }\r
-\r
- return out.toString();\r
- }\r
-}\r
+/*
+ * 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
+ * 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 java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+public class ClustalFile
+ extends AlignFile
+{
+
+ public ClustalFile()
+ {
+ }
+
+ public ClustalFile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+ public ClustalFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+ public void initData()
+ {
+ super.initData();
+ }
+
+ public void parse()
+ throws IOException
+ {
+ int i = 0;
+ boolean flag = false;
+
+ Vector headers = new Vector();
+ Hashtable seqhash = new Hashtable();
+ StringBuffer tempseq;
+ String line, id;
+ StringTokenizer str;
+
+ try
+ {
+ while ( (line = nextLine()) != null)
+ {
+ if (line.indexOf(" ") != 0)
+ {
+ str = new StringTokenizer(line, " ");
+
+ if (str.hasMoreTokens())
+ {
+ id = str.nextToken();
+
+ if (id.equalsIgnoreCase("CLUSTAL"))
+ {
+ flag = true;
+ }
+ else
+ {
+ if (flag)
+ {
+ 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());
+ }
+ }
+ }
+ }
+ else
+ {
+ flag = true;
+ }
+ }
+ }
+ }
+ 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));
+ }
+ }
+ }
+ }
+
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ public 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 = printId(s[i]);
+
+ 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(printId(s[j]) + " "));
+
+ int start = i * len;
+ int end = start + len;
+
+ if ( (end < s[j].getSequence().length) &&
+ (start < s[j].getSequence().length))
+ {
+ out.append(s[j].getSequenceAsString(start, end));
+ }
+ else
+ {
+ if (start < s[j].getSequence().length)
+ {
+ out.append(s[j].getSequenceAsString().substring(start));
+ }
+ }
+
+ out.append("\n");
+ j++;
+ }
+
+ out.append("\n");
+ }
+
+ return out.toString();
+ }
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FastaFile\r
- extends AlignFile\r
-{\r
- /**\r
- * Length of a sequence line\r
- */\r
- int len = 72;\r
-\r
- StringBuffer out;\r
-\r
- /**\r
- * Creates a new FastaFile object.\r
- */\r
- public FastaFile()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new FastaFile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public FastaFile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public void parse()\r
- throws IOException\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- boolean firstLine = true;\r
-\r
- String line;\r
- Sequence seq = null;\r
-\r
- boolean annotation = false;\r
-\r
- while ( (line = nextLine()) != null)\r
- {\r
- line = line.trim();\r
- if (line.length() > 0)\r
- {\r
- if (line.charAt(0) == '>')\r
- {\r
- if (line.startsWith(">#_"))\r
- {\r
- if (annotation)\r
- {\r
- Annotation[] anots = new Annotation[sb.length()];\r
- String anotString = sb.toString();\r
- for (int i = 0; i < sb.length(); i++)\r
- {\r
- anots[i] = new Annotation(anotString.substring(i, i + 1),\r
- null,\r
- ' ', 0);\r
- }\r
- AlignmentAnnotation aa = new AlignmentAnnotation(\r
- seq.getName().substring(2), seq.getDescription(),\r
- anots);\r
-\r
- annotations.addElement(aa);\r
- }\r
- }\r
- else\r
- {\r
- annotation = false;\r
- }\r
-\r
- if (!firstLine)\r
- {\r
- seq.setSequence(sb.toString());\r
-\r
- if (!annotation)\r
- {\r
- seqs.addElement(seq);\r
- }\r
- }\r
-\r
- seq = parseId(line.substring(1));\r
- firstLine = false;\r
-\r
- sb = new StringBuffer();\r
-\r
- if (line.startsWith(">#_"))\r
- {\r
- annotation = true;\r
- }\r
- }\r
- else\r
- {\r
- sb.append(line);\r
- }\r
- }\r
- }\r
-\r
- if (annotation)\r
- {\r
- Annotation[] anots = new Annotation[sb.length()];\r
- String anotString = sb.toString();\r
- for (int i = 0; i < sb.length(); i++)\r
- {\r
- anots[i] = new Annotation(anotString.substring(i, i + 1),\r
- null,\r
- ' ', 0);\r
- }\r
- AlignmentAnnotation aa = new AlignmentAnnotation(\r
- seq.getName().substring(2), seq.getDescription(),\r
- anots);\r
-\r
- annotations.addElement(aa);\r
- }\r
-\r
- else if (!firstLine)\r
- {\r
- seq.setSequence(sb.toString());\r
- seqs.addElement(seq);\r
- }\r
- }\r
-\r
- /**\r
- * called by AppletFormatAdapter to generate\r
- * an annotated alignment, rather than bare\r
- * sequences.\r
- * @param al\r
- */\r
- public void addAnnotations(Alignment al)\r
- {\r
- addProperties(al);\r
- for (int i = 0; i < annotations.size(); i++)\r
- {\r
- AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i);\r
- aa.setPadGaps(true, al.getGapCharacter());\r
- al.addAnnotation( aa );\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- * @param gaps DOCUMENT ME!\r
- * @param displayId DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print(SequenceI[] s)\r
- {\r
- out = new StringBuffer();\r
- int i = 0;\r
-\r
- while ( (i < s.length) && (s[i] != null))\r
- {\r
- out.append(">" + printId(s[i]));\r
- if (s[i].getDescription() != null)\r
- {\r
- out.append(" " + s[i].getDescription());\r
- }\r
-\r
- out.append("\n");\r
-\r
- int nochunks = (s[i].getLength() / len) + 1;\r
-\r
- for (int j = 0; j < nochunks; j++)\r
- {\r
- int start = j * len;\r
- int end = start + len;\r
-\r
- if (end < s[i].getLength())\r
- {\r
- out.append(s[i].getSequenceAsString(start, end) + "\n");\r
- }\r
- else if (start < s[i].getLength())\r
- {\r
- out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");\r
- }\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-}\r
+/*
+ * 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
+ * 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 java.io.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FastaFile
+ extends AlignFile
+{
+ /**
+ * Length of a sequence line
+ */
+ int len = 72;
+
+ StringBuffer out;
+
+ /**
+ * Creates a new FastaFile object.
+ */
+ public FastaFile()
+ {
+ }
+
+ /**
+ * Creates a new FastaFile object.
+ *
+ * @param inFile DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public FastaFile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public FastaFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void parse()
+ throws IOException
+ {
+ StringBuffer sb = new StringBuffer();
+ boolean firstLine = true;
+
+ String line;
+ Sequence seq = null;
+
+ boolean annotation = false;
+
+ while ( (line = nextLine()) != null)
+ {
+ line = line.trim();
+ if (line.length() > 0)
+ {
+ if (line.charAt(0) == '>')
+ {
+ if (line.startsWith(">#_"))
+ {
+ if (annotation)
+ {
+ Annotation[] anots = new Annotation[sb.length()];
+ String anotString = sb.toString();
+ for (int i = 0; i < sb.length(); i++)
+ {
+ anots[i] = new Annotation(anotString.substring(i, i + 1),
+ null,
+ ' ', 0);
+ }
+ AlignmentAnnotation aa = new AlignmentAnnotation(
+ seq.getName().substring(2), seq.getDescription(),
+ anots);
+
+ annotations.addElement(aa);
+ }
+ }
+ else
+ {
+ annotation = false;
+ }
+
+ if (!firstLine)
+ {
+ seq.setSequence(sb.toString());
+
+ if (!annotation)
+ {
+ seqs.addElement(seq);
+ }
+ }
+
+ seq = parseId(line.substring(1));
+ firstLine = false;
+
+ sb = new StringBuffer();
+
+ if (line.startsWith(">#_"))
+ {
+ annotation = true;
+ }
+ }
+ else
+ {
+ sb.append(line);
+ }
+ }
+ }
+
+ if (annotation)
+ {
+ Annotation[] anots = new Annotation[sb.length()];
+ String anotString = sb.toString();
+ for (int i = 0; i < sb.length(); i++)
+ {
+ anots[i] = new Annotation(anotString.substring(i, i + 1),
+ null,
+ ' ', 0);
+ }
+ AlignmentAnnotation aa = new AlignmentAnnotation(
+ seq.getName().substring(2), seq.getDescription(),
+ anots);
+
+ annotations.addElement(aa);
+ }
+
+ else if (!firstLine)
+ {
+ seq.setSequence(sb.toString());
+ seqs.addElement(seq);
+ }
+ }
+
+ /**
+ * called by AppletFormatAdapter to generate
+ * an annotated alignment, rather than bare
+ * sequences.
+ * @param al
+ */
+ public void addAnnotations(Alignment al)
+ {
+ addProperties(al);
+ for (int i = 0; i < annotations.size(); i++)
+ {
+ AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i);
+ aa.setPadGaps(true, al.getGapCharacter());
+ al.addAnnotation( aa );
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ * @param len DOCUMENT ME!
+ * @param gaps DOCUMENT ME!
+ * @param displayId DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print(SequenceI[] s)
+ {
+ out = new StringBuffer();
+ int i = 0;
+
+ while ( (i < s.length) && (s[i] != null))
+ {
+ out.append(">" + printId(s[i]));
+ if (s[i].getDescription() != null)
+ {
+ out.append(" " + s[i].getDescription());
+ }
+
+ out.append("\n");
+
+ int nochunks = (s[i].getLength() / len) + 1;
+
+ for (int j = 0; j < nochunks; j++)
+ {
+ int start = j * len;
+ int end = start + len;
+
+ if (end < s[i].getLength())
+ {
+ out.append(s[i].getSequenceAsString(start, end) + "\n");
+ }
+ else if (start < s[i].getLength())
+ {
+ out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
+ }
+ }
+
+ i++;
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+}
{\r
super(inFile, type);\r
}\r
+ public FeaturesFile(FileParse source) throws IOException\r
+ {\r
+ super(source);\r
+ }\r
\r
/**\r
* The Application can render HTML, but the applet will\r
public class FileParse
{
public File inFile=null;
+ public int index = 1; // sequence counter for FileParse object created from same data source
protected char suffixSeparator = '#';
/**
* '#' separated string tagged on to end of filename
{
}
/**
+ * Create a new FileParse instance reading from the same datasource starting at the current position.
+ * WARNING! Subsequent reads from either object will affect the read position of the other, but not
+ * the error state.
+ *
+ * @param from
+ */
+ public FileParse(FileParse from) throws IOException
+ {
+ if (from==null)
+ {
+ throw new Error("Implementation error. Null FileParse in copy constructor");
+ }
+ if (from==this)
+ return;
+ index = ++from.index;
+ inFile = from.inFile;
+ suffixSeparator = from.suffixSeparator;
+ suffix = from.suffix;
+ errormessage = from.errormessage; // inherit potential error messages
+ error = false; // reset any error condition.
+ type = from.type;
+ dataIn = from.dataIn;
+ if (dataIn!=null)
+ {
+ mark();
+ }
+ }
+ /**
* Attempt to open a file as a datasource.
* Sets error and errormessage if fileStr was invalid.
* @param fileStr
error=false;
dataIn.mark(READAHEAD_LIMIT);
}
+ /**
+ * mark the current position in the source as start
+ * for the purposes of it being analysed by IdentifyFile().identify
+ * @throws IOException
+ */
+ public void mark() throws IOException
+ {
+ if (dataIn!=null)
+ {
+ dataIn.mark(READAHEAD_LIMIT);
+ } else {
+ throw new IOException("Unitialised Source Stream");
+ }
+ }
public String nextLine()
throws IOException
{
public String getWarningMessage() {
return warningMessage;
}
+ public String getInFile()
+ {
+ if (inFile!=null)
+ {
+ return inFile.getAbsolutePath()+" ("+index+")";
+ }
+ else
+ {
+ return "From Paste + ("+index+")";
+ }
+ }
}
{
super(inFile, type);
}
-
+ public JPredFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
/**
* DOCUMENT ME!
*
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class MSFfile\r
- extends AlignFile\r
-{\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- */\r
- public MSFfile()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public MSFfile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void parse()\r
- throws IOException\r
- {\r
- int i = 0;\r
- boolean seqFlag = false;\r
- String key = new String();\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
- String line;\r
-\r
- try\r
- {\r
- while ( (line = nextLine()) != null)\r
- {\r
- StringTokenizer str = new StringTokenizer(line);\r
-\r
- while (str.hasMoreTokens())\r
- {\r
- String inStr = str.nextToken();\r
-\r
- //If line has header information add to the headers vector\r
- if (inStr.indexOf("Name:") != -1)\r
- {\r
- key = str.nextToken();\r
- headers.addElement(key);\r
- }\r
-\r
- //if line has // set SeqFlag to 1 so we know sequences are coming\r
- if (inStr.indexOf("//") != -1)\r
- {\r
- seqFlag = true;\r
- }\r
-\r
- //Process lines as sequence lines if seqFlag is set\r
- if ( (inStr.indexOf("//") == -1) && (seqFlag == true))\r
- {\r
- //seqeunce id is the first field\r
- key = inStr;\r
-\r
- StringBuffer tempseq;\r
-\r
- //Get sequence from hash if it exists\r
- if (seqhash.containsKey(key))\r
- {\r
- tempseq = (StringBuffer) seqhash.get(key);\r
- }\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(key, tempseq);\r
- }\r
-\r
- //loop through the rest of the words\r
- while (str.hasMoreTokens())\r
- {\r
- //append the word to the sequence\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
- }\r
- catch (IOException e)\r
- {\r
- System.err.println("Exception parsing MSFFile " + e);\r
- e.printStackTrace();\r
- }\r
-\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++)\r
- {\r
- if (seqhash.get(headers.elementAt(i)) != null)\r
- {\r
- String head = headers.elementAt(i).toString();\r
- String seq = seqhash.get(head).toString();\r
-\r
- if (maxLength < head.length())\r
- {\r
- maxLength = head.length();\r
- }\r
-\r
- // Replace ~ with a sensible gap character\r
- seq = seq.replace('~', '-');\r
-\r
- Sequence newSeq = parseId(head);\r
-\r
- newSeq.setSequence(seq);\r
-\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- System.err.println("MSFFile Parser: Can't find sequence for " +\r
- headers.elementAt(i));\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int checkSum(String seq)\r
- {\r
- int check = 0;\r
- String sequence = seq.toUpperCase();\r
-\r
- for (int i = 0; i < sequence.length(); i++)\r
- {\r
- try\r
- {\r
-\r
- int value = sequence.charAt(i);\r
- if (value != -1)\r
- {\r
- check += (i % 57 + 1) * value;\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Exception during MSF Checksum calculation");\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- return check % 10000;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param is_NA DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print(SequenceI[] seqs)\r
- {\r
-\r
- boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);\r
-\r
- SequenceI[] s = new SequenceI[seqs.length];\r
-\r
- StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
- "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
-\r
- int max = 0;\r
- int maxid = 0;\r
- int i = 0;\r
-\r
- while ( (i < seqs.length) && (seqs[i] != null))\r
- {\r
- // Replace all internal gaps with . and external spaces with ~\r
- s[i] = new Sequence(seqs[i].getName(),\r
- seqs[i].getSequenceAsString().replace('-', '.'));\r
-\r
- StringBuffer sb = new StringBuffer();\r
- sb.append(s[i].getSequence());\r
-\r
- for (int ii = 0; ii < sb.length(); ii++)\r
- {\r
- if (sb.charAt(ii) == '.')\r
- {\r
- sb.setCharAt(ii, '~');\r
- }\r
- else\r
- {\r
- break;\r
- }\r
- }\r
-\r
- for (int ii = sb.length() - 1; ii > 0; ii--)\r
- {\r
- if (sb.charAt(ii) == '.')\r
- {\r
- sb.setCharAt(ii, '~');\r
- }\r
- else\r
- {\r
- break;\r
- }\r
- }\r
-\r
- s[i].setSequence(sb.toString());\r
-\r
- if (s[i].getSequence().length > max)\r
- {\r
- max = s[i].getSequence().length;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- Format maxLenpad = new Format("%" + (new String("" + max)).length() +\r
- "d");\r
- Format maxChkpad = new Format("%" + (new String("1" + max)).length() +\r
- "d");\r
- i = 0;\r
-\r
- int bigChecksum = 0;\r
- int[] checksums = new int[s.length];\r
- while (i < s.length)\r
- {\r
- checksums[i] = checkSum(s[i].getSequenceAsString());\r
- bigChecksum += checksums[i];\r
- i++;\r
- }\r
-\r
- long maxNB = 0;\r
- out.append(" MSF: " + s[0].getSequence().length + " Type: " +\r
- (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) +\r
- " ..\n\n\n");\r
-\r
- String[] nameBlock = new String[s.length];\r
- String[] idBlock = new String[s.length];\r
-\r
- i = 0;\r
- while ( (i < s.length) && (s[i] != null))\r
- {\r
-\r
- nameBlock[i] = new String(" Name: " + printId(s[i]) + " ");\r
-\r
- idBlock[i] = new String("Len: " +\r
- maxLenpad.form(s[i].getSequence().length) +\r
- " Check: " +\r
- maxChkpad.form(checksums[i]) + " Weight: 1.00\n");\r
-\r
- if (s[i].getName().length() > maxid)\r
- {\r
- maxid = s[i].getName().length();\r
- }\r
-\r
- if (nameBlock[i].length() > maxNB)\r
- {\r
- maxNB = nameBlock[i].length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if (maxid < 10)\r
- {\r
- maxid = 10;\r
- }\r
-\r
- if (maxNB < 15)\r
- {\r
- maxNB = 15;\r
- }\r
-\r
- Format nbFormat = new Format("%-" + maxNB + "s");\r
-\r
- for (i = 0; (i < s.length) && (s[i] != null); i++)\r
- {\r
- out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);\r
- }\r
-\r
- maxid++;\r
- out.append("\n\n//\n\n");\r
-\r
- int len = 50;\r
-\r
- int nochunks = (max / len) + 1;\r
-\r
- if ( (max % len) == 0)\r
- {\r
- nochunks--;\r
- }\r
-\r
- for (i = 0; i < nochunks; i++)\r
- {\r
- int j = 0;\r
-\r
- while ( (j < s.length) && (s[j] != null))\r
- {\r
- String name = printId(s[j]);\r
-\r
- out.append(new Format("%-" + maxid + "s").form(name + " "));\r
-\r
- for (int k = 0; k < 5; k++)\r
- {\r
- int start = (i * 50) + (k * 10);\r
- int end = start + 10;\r
-\r
- if ( (end < s[j].getSequence().length) &&\r
- (start < s[j].getSequence().length))\r
- {\r
- out.append(s[j].getSequence(start, end));\r
-\r
- if (k < 4)\r
- {\r
- out.append(" ");\r
- }\r
- else\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- else\r
- {\r
- if (start < s[j].getSequence().length)\r
- {\r
- out.append(s[j].getSequenceAsString().substring(start));\r
- out.append("\n");\r
- }\r
- else\r
- {\r
- if (k == 0)\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- }\r
- }\r
-\r
- j++;\r
- }\r
-\r
- out.append("\n");\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-}\r
+/*
+ * 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
+ * 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 java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class MSFfile
+ extends AlignFile
+{
+
+ /**
+ * Creates a new MSFfile object.
+ */
+ public MSFfile()
+ {
+ }
+
+ /**
+ * Creates a new MSFfile object.
+ *
+ * @param inFile DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public MSFfile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public MSFfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+{
+ // TODO Auto-generated constructor stub
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void parse()
+ throws IOException
+ {
+ int i = 0;
+ boolean seqFlag = false;
+ String key = new String();
+ Vector headers = new Vector();
+ Hashtable seqhash = new Hashtable();
+ String line;
+
+ try
+ {
+ while ( (line = nextLine()) != null)
+ {
+ StringTokenizer str = new StringTokenizer(line);
+
+ while (str.hasMoreTokens())
+ {
+ String inStr = str.nextToken();
+
+ //If line has header information add to the headers vector
+ if (inStr.indexOf("Name:") != -1)
+ {
+ key = str.nextToken();
+ headers.addElement(key);
+ }
+
+ //if line has // set SeqFlag to 1 so we know sequences are coming
+ if (inStr.indexOf("//") != -1)
+ {
+ seqFlag = true;
+ }
+
+ //Process lines as sequence lines if seqFlag is set
+ if ( (inStr.indexOf("//") == -1) && (seqFlag == true))
+ {
+ //seqeunce id is the first field
+ key = inStr;
+
+ StringBuffer tempseq;
+
+ //Get sequence from hash if it exists
+ if (seqhash.containsKey(key))
+ {
+ tempseq = (StringBuffer) seqhash.get(key);
+ }
+ else
+ {
+ tempseq = new StringBuffer();
+ seqhash.put(key, tempseq);
+ }
+
+ //loop through the rest of the words
+ while (str.hasMoreTokens())
+ {
+ //append the word to the sequence
+ tempseq.append(str.nextToken());
+ }
+ }
+ }
+ }
+ }
+ catch (IOException e)
+ {
+ System.err.println("Exception parsing MSFFile " + e);
+ e.printStackTrace();
+ }
+
+ this.noSeqs = headers.size();
+
+ //Add sequences to the hash
+ for (i = 0; i < headers.size(); i++)
+ {
+ if (seqhash.get(headers.elementAt(i)) != null)
+ {
+ String head = headers.elementAt(i).toString();
+ String seq = seqhash.get(head).toString();
+
+ if (maxLength < head.length())
+ {
+ maxLength = head.length();
+ }
+
+ // Replace ~ with a sensible gap character
+ seq = seq.replace('~', '-');
+
+ Sequence newSeq = parseId(head);
+
+ newSeq.setSequence(seq);
+
+ seqs.addElement(newSeq);
+ }
+ else
+ {
+ System.err.println("MSFFile Parser: Can't find sequence for " +
+ headers.elementAt(i));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int checkSum(String seq)
+ {
+ int check = 0;
+ String sequence = seq.toUpperCase();
+
+ for (int i = 0; i < sequence.length(); i++)
+ {
+ try
+ {
+
+ int value = sequence.charAt(i);
+ if (value != -1)
+ {
+ check += (i % 57 + 1) * value;
+ }
+ }
+ catch (Exception e)
+ {
+ System.err.println("Exception during MSF Checksum calculation");
+ e.printStackTrace();
+ }
+ }
+
+ return check % 10000;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ * @param is_NA DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print(SequenceI[] seqs)
+ {
+
+ boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+
+ SequenceI[] s = new SequenceI[seqs.length];
+
+ StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
+ "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+
+ int max = 0;
+ int maxid = 0;
+ int i = 0;
+
+ while ( (i < seqs.length) && (seqs[i] != null))
+ {
+ // Replace all internal gaps with . and external spaces with ~
+ s[i] = new Sequence(seqs[i].getName(),
+ seqs[i].getSequenceAsString().replace('-', '.'));
+
+ StringBuffer sb = new StringBuffer();
+ sb.append(s[i].getSequence());
+
+ for (int ii = 0; ii < sb.length(); ii++)
+ {
+ if (sb.charAt(ii) == '.')
+ {
+ sb.setCharAt(ii, '~');
+ }
+ else
+ {
+ break;
+ }
+ }
+
+ for (int ii = sb.length() - 1; ii > 0; ii--)
+ {
+ if (sb.charAt(ii) == '.')
+ {
+ sb.setCharAt(ii, '~');
+ }
+ else
+ {
+ break;
+ }
+ }
+
+ s[i].setSequence(sb.toString());
+
+ if (s[i].getSequence().length > max)
+ {
+ max = s[i].getSequence().length;
+ }
+
+ i++;
+ }
+
+ Format maxLenpad = new Format("%" + (new String("" + max)).length() +
+ "d");
+ Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
+ "d");
+ i = 0;
+
+ int bigChecksum = 0;
+ int[] checksums = new int[s.length];
+ while (i < s.length)
+ {
+ checksums[i] = checkSum(s[i].getSequenceAsString());
+ bigChecksum += checksums[i];
+ i++;
+ }
+
+ long maxNB = 0;
+ out.append(" MSF: " + s[0].getSequence().length + " Type: " +
+ (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) +
+ " ..\n\n\n");
+
+ String[] nameBlock = new String[s.length];
+ String[] idBlock = new String[s.length];
+
+ i = 0;
+ while ( (i < s.length) && (s[i] != null))
+ {
+
+ nameBlock[i] = new String(" Name: " + printId(s[i]) + " ");
+
+ idBlock[i] = new String("Len: " +
+ maxLenpad.form(s[i].getSequence().length) +
+ " Check: " +
+ maxChkpad.form(checksums[i]) + " Weight: 1.00\n");
+
+ if (s[i].getName().length() > maxid)
+ {
+ maxid = s[i].getName().length();
+ }
+
+ if (nameBlock[i].length() > maxNB)
+ {
+ maxNB = nameBlock[i].length();
+ }
+
+ i++;
+ }
+
+ if (maxid < 10)
+ {
+ maxid = 10;
+ }
+
+ if (maxNB < 15)
+ {
+ maxNB = 15;
+ }
+
+ Format nbFormat = new Format("%-" + maxNB + "s");
+
+ for (i = 0; (i < s.length) && (s[i] != null); i++)
+ {
+ out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);
+ }
+
+ maxid++;
+ out.append("\n\n//\n\n");
+
+ int len = 50;
+
+ int nochunks = (max / len) + 1;
+
+ if ( (max % len) == 0)
+ {
+ nochunks--;
+ }
+
+ for (i = 0; i < nochunks; i++)
+ {
+ int j = 0;
+
+ while ( (j < s.length) && (s[j] != null))
+ {
+ String name = printId(s[j]);
+
+ out.append(new Format("%-" + maxid + "s").form(name + " "));
+
+ for (int k = 0; k < 5; k++)
+ {
+ int start = (i * 50) + (k * 10);
+ int end = start + 10;
+
+ if ( (end < s[j].getSequence().length) &&
+ (start < s[j].getSequence().length))
+ {
+ out.append(s[j].getSequence(start, end));
+
+ if (k < 4)
+ {
+ out.append(" ");
+ }
+ else
+ {
+ out.append("\n");
+ }
+ }
+ else
+ {
+ if (start < s[j].getSequence().length)
+ {
+ out.append(s[j].getSequenceAsString().substring(start));
+ out.append("\n");
+ }
+ else
+ {
+ if (k == 0)
+ {
+ out.append("\n");
+ }
+ }
+ }
+ }
+
+ j++;
+ }
+
+ out.append("\n");
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+}
{
super(inFile, type);
}
-
+ public NewickFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
/**
* Creates a new NewickFile object.
*
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class PIRFile\r
- extends AlignFile\r
-{\r
- public static boolean useModellerOutput = false;\r
-\r
- Vector words = new Vector(); //Stores the words in a line after splitting\r
-\r
- public PIRFile()\r
- {\r
- }\r
-\r
- public PIRFile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public void parse()\r
- throws IOException\r
- {\r
- StringBuffer sequence;\r
- String line = null;\r
- ModellerDescription md;\r
-\r
- while ( (line = nextLine()) != null)\r
- {\r
- if (line.length() == 0)\r
- {\r
- //System.out.println("blank line");\r
- continue;\r
- }\r
- if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)\r
- {\r
- continue;\r
- }\r
- Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
-\r
- sequence = new StringBuffer();\r
-\r
- newSeq.setDescription(nextLine()); // this is the title line\r
-\r
- boolean starFound = false;\r
-\r
- while (!starFound)\r
- {\r
- line = nextLine();\r
- sequence.append(line);\r
-\r
- if (line == null)\r
- {\r
- break;\r
- }\r
-\r
- if (line.indexOf("*") > -1)\r
- {\r
- starFound = true;\r
- }\r
- }\r
-\r
- if (sequence.length() > 0)\r
- {\r
- sequence.setLength(sequence.length() - 1);\r
- newSeq.setSequence(sequence.toString());\r
-\r
- seqs.addElement(newSeq);\r
-\r
- md = new ModellerDescription(newSeq.\r
- getDescription());\r
- md.updateSequenceI(newSeq);\r
- }\r
- }\r
- }\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-\r
- public String print(SequenceI[] s)\r
- {\r
- boolean is_NA = jalview.util.Comparison.isNucleotide(s);\r
- int len = 72;\r
- StringBuffer out = new StringBuffer();\r
- int i = 0;\r
- ModellerDescription md;\r
-\r
- while ( (i < s.length) && (s[i] != null))\r
- {\r
- String seq = s[i].getSequenceAsString();\r
- seq = seq + "*";\r
-\r
- if (is_NA)\r
- {\r
- // modeller doesn't really do nucleotides, so we don't do anything fancy\r
- // Official tags area as follows, for now we'll use P1 and DL\r
- // Protein (complete) P1\r
- // Protein (fragment) F1\r
- // DNA (linear) Dl\r
- // DNA (circular) DC\r
- // RNA (linear) RL\r
- // RNA (circular) RC\r
- // tRNA N3\r
- // other functional RNA N1\r
-\r
- out.append(">N1;" + s[i].getName() + "\n");\r
- if (s[i].getDescription() == null)\r
- {\r
- out.append(s[i].getName() + " " +\r
- (s[i].getEnd() - s[i].getStart() + 1));\r
- out.append(is_NA ? " bases\n" : " residues\n");\r
- }\r
- else\r
- {\r
- out.append(s[i].getDescription() + "\n");\r
- }\r
- }\r
- else\r
- {\r
-\r
- if (useModellerOutput)\r
- {\r
- out.append(">P1;" + s[i].getName() + "\n");\r
- md = new ModellerDescription(s[i]);\r
- out.append(md.getDescriptionLine() + "\n");\r
- }\r
- else\r
- {\r
- out.append(">P1;" + printId(s[i]) + "\n");\r
- if (s[i].getDescription() != null)\r
- {\r
- out.append(s[i].getDescription() + "\n");\r
- }\r
- else\r
- {\r
- out.append(s[i].getName() + " "\r
- + (s[i].getEnd() - s[i].getStart() + 1)\r
- + " residues\n");\r
- }\r
- }\r
- }\r
- int nochunks = (seq.length() / len) + 1;\r
-\r
- for (int j = 0; j < nochunks; j++)\r
- {\r
- int start = j * len;\r
- int end = start + len;\r
-\r
- if (end < seq.length())\r
- {\r
- out.append(seq.substring(start, end) + "\n");\r
- }\r
- else if (start < seq.length())\r
- {\r
- out.append(seq.substring(start) + "\n");\r
- }\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
-}\r
+/*
+ * 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
+ * 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 java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+
+public class PIRFile
+ extends AlignFile
+{
+ public static boolean useModellerOutput = false;
+
+ Vector words = new Vector(); //Stores the words in a line after splitting
+
+ public PIRFile()
+ {
+ }
+
+ public PIRFile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+ public PIRFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+ public void parse()
+ throws IOException
+ {
+ StringBuffer sequence;
+ String line = null;
+ ModellerDescription md;
+
+ while ( (line = nextLine()) != null)
+ {
+ if (line.length() == 0)
+ {
+ //System.out.println("blank line");
+ continue;
+ }
+ if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
+ {
+ continue;
+ }
+ Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
+
+ sequence = new StringBuffer();
+
+ newSeq.setDescription(nextLine()); // this is the title line
+
+ boolean starFound = false;
+
+ while (!starFound)
+ {
+ line = nextLine();
+ sequence.append(line);
+
+ if (line == null)
+ {
+ break;
+ }
+
+ if (line.indexOf("*") > -1)
+ {
+ starFound = true;
+ }
+ }
+
+ if (sequence.length() > 0)
+ {
+ sequence.setLength(sequence.length() - 1);
+ newSeq.setSequence(sequence.toString());
+
+ seqs.addElement(newSeq);
+
+ md = new ModellerDescription(newSeq.
+ getDescription());
+ md.updateSequenceI(newSeq);
+ }
+ }
+ }
+
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ public String print(SequenceI[] s)
+ {
+ boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+ int len = 72;
+ StringBuffer out = new StringBuffer();
+ int i = 0;
+ ModellerDescription md;
+
+ while ( (i < s.length) && (s[i] != null))
+ {
+ String seq = s[i].getSequenceAsString();
+ seq = seq + "*";
+
+ if (is_NA)
+ {
+ // modeller doesn't really do nucleotides, so we don't do anything fancy
+ // Official tags area as follows, for now we'll use P1 and DL
+ // Protein (complete) P1
+ // Protein (fragment) F1
+ // DNA (linear) Dl
+ // DNA (circular) DC
+ // RNA (linear) RL
+ // RNA (circular) RC
+ // tRNA N3
+ // other functional RNA N1
+
+ out.append(">N1;" + s[i].getName() + "\n");
+ if (s[i].getDescription() == null)
+ {
+ out.append(s[i].getName() + " " +
+ (s[i].getEnd() - s[i].getStart() + 1));
+ out.append(is_NA ? " bases\n" : " residues\n");
+ }
+ else
+ {
+ out.append(s[i].getDescription() + "\n");
+ }
+ }
+ else
+ {
+
+ if (useModellerOutput)
+ {
+ out.append(">P1;" + s[i].getName() + "\n");
+ md = new ModellerDescription(s[i]);
+ out.append(md.getDescriptionLine() + "\n");
+ }
+ else
+ {
+ out.append(">P1;" + printId(s[i]) + "\n");
+ if (s[i].getDescription() != null)
+ {
+ out.append(s[i].getDescription() + "\n");
+ }
+ else
+ {
+ out.append(s[i].getName() + " "
+ + (s[i].getEnd() - s[i].getStart() + 1)
+ + " residues\n");
+ }
+ }
+ }
+ int nochunks = (seq.length() / len) + 1;
+
+ for (int j = 0; j < nochunks; j++)
+ {
+ int start = j * len;
+ int end = start + len;
+
+ if (end < seq.length())
+ {
+ out.append(seq.substring(start, end) + "\n");
+ }
+ else if (start < seq.length())
+ {
+ out.append(seq.substring(start) + "\n");
+ }
+ }
+
+ i++;
+ }
+
+ return out.toString();
+ }
+
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-\r
-public class PfamFile\r
- extends AlignFile\r
-{\r
-\r
- public PfamFile()\r
- {\r
- }\r
-\r
- public PfamFile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public void initData()\r
- {\r
- super.initData();\r
- }\r
-\r
- public void parse()\r
- throws IOException\r
- {\r
- int i = 0;\r
- String line;\r
-\r
- Hashtable seqhash = new Hashtable();\r
- Vector headers = new Vector();\r
-\r
- while ( (line = nextLine()) != null)\r
- {\r
- if (line.indexOf(" ") != 0)\r
- {\r
- if (line.indexOf("#") != 0)\r
- {\r
- StringTokenizer str = new StringTokenizer(line, " ");\r
- String id = "";\r
-\r
- if (str.hasMoreTokens())\r
- {\r
- id = str.nextToken();\r
-\r
- StringBuffer tempseq;\r
-\r
- if (seqhash.containsKey(id))\r
- {\r
- tempseq = (StringBuffer) seqhash.get(id);\r
- }\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(id, tempseq);\r
- }\r
-\r
- if (! (headers.contains(id)))\r
- {\r
- headers.addElement(id);\r
- }\r
-\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
-\r
- this.noSeqs = headers.size();\r
-\r
- if (noSeqs < 1)\r
- {\r
- throw new IOException("No sequences found (PFAM input)");\r
- }\r
-\r
- for (i = 0; i < headers.size(); i++)\r
- {\r
- if (seqhash.get(headers.elementAt(i)) != null)\r
- {\r
- if (maxLength < seqhash.get(headers.elementAt(i)).toString()\r
- .length())\r
- {\r
- maxLength = seqhash.get(headers.elementAt(i)).toString()\r
- .length();\r
- }\r
-\r
- Sequence newSeq = parseId(headers.elementAt(i).toString());\r
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).\r
- toString());\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- System.err.println("PFAM File reader: Can't find sequence for " +\r
- headers.elementAt(i));\r
- }\r
- }\r
- }\r
-\r
- public String print(SequenceI[] s)\r
- {\r
- StringBuffer out = new StringBuffer("");\r
-\r
- int max = 0;\r
- int maxid = 0;\r
-\r
- int i = 0;\r
-\r
- while ( (i < s.length) && (s[i] != null))\r
- {\r
- String tmp = printId(s[i]);\r
-\r
- if (s[i].getSequence().length > max)\r
- {\r
- max = s[i].getSequence().length;\r
- }\r
-\r
- if (tmp.length() > maxid)\r
- {\r
- maxid = tmp.length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if (maxid < 15)\r
- {\r
- maxid = 15;\r
- }\r
-\r
- int j = 0;\r
-\r
- while ( (j < s.length) && (s[j] != null))\r
- {\r
- out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));\r
-\r
- out.append(s[j].getSequenceAsString() + "\n");\r
- j++;\r
- }\r
-\r
- out.append("\n");\r
-\r
- return out.toString();\r
- }\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-}\r
+/*
+ * 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
+ * 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 java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+public class PfamFile
+ extends AlignFile
+{
+
+ public PfamFile()
+ {
+ }
+
+ public PfamFile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+ public PfamFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+ public void initData()
+ {
+ super.initData();
+ }
+
+ 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();
+ }
+
+ Sequence newSeq = parseId(headers.elementAt(i).toString());
+ newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
+ toString());
+ seqs.addElement(newSeq);
+ }
+ else
+ {
+ System.err.println("PFAM File reader: Can't find sequence for " +
+ headers.elementAt(i));
+ }
+ }
+ }
+
+ public 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 = printId(s[i]);
+
+ 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(printId(s[j]) + " "));
+
+ out.append(s[j].getSequenceAsString() + "\n");
+ j++;
+ }
+
+ out.append("\n");
+
+ return out.toString();
+ }
+
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-/**\r
- * <p>Title: </p>\r
- * PileUpfile\r
- * <p>Description: </p>\r
- *\r
- * Read and write PileUp style MSF Files.\r
- * This used to be the MSFFile class, and was written according to the EBI's idea\r
- * of a subset of the MSF alignment format. But, that was updated to reflect current\r
- * GCG style IO fashion, as found in Emboss (thanks David Martin!)\r
- *\r
- **/\r
-import java.io.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-\r
-public class PileUpfile\r
- extends MSFfile\r
-{\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- */\r
- public PileUpfile()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public PileUpfile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-\r
- public String print(SequenceI[] s)\r
- {\r
- StringBuffer out = new StringBuffer("PileUp\n\n");\r
-\r
- int max = 0;\r
- int maxid = 0;\r
-\r
- int i = 0;\r
- int bigChecksum = 0;\r
- int[] checksums = new int[s.length];\r
- while (i < s.length)\r
- {\r
- checksums[i] = checkSum(s[i].getSequenceAsString());\r
- bigChecksum += checksums[i];\r
- i++;\r
- }\r
-\r
- out.append(" MSF: " + s[0].getSequence().length +\r
- " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n");\r
-\r
- i = 0;\r
- while ( (i < s.length) && (s[i] != null))\r
- {\r
- String seq = s[i].getSequenceAsString();\r
- out.append(" Name: " + printId(s[i]) +\r
- " oo Len: " +\r
- seq.length() + " Check: " + checksums[i] +\r
- " Weight: 1.00\n");\r
-\r
- if (seq.length() > max)\r
- {\r
- max = seq.length();\r
- }\r
-\r
- if (s[i].getName().length() > maxid)\r
- {\r
- maxid = s[i].getName().length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if (maxid < 10)\r
- {\r
- maxid = 10;\r
- }\r
-\r
- maxid++;\r
- out.append("\n\n//\n\n");\r
-\r
- int len = 50;\r
-\r
- int nochunks = (max / len) + 1;\r
-\r
- if ( (max % len) == 0)\r
- {\r
- nochunks--;\r
- }\r
-\r
- for (i = 0; i < nochunks; i++)\r
- {\r
- int j = 0;\r
-\r
- while ( (j < s.length) && (s[j] != null))\r
- {\r
- String name = printId(s[j]);\r
-\r
- out.append(new Format("%-" + maxid + "s").form(name + " "));\r
-\r
- for (int k = 0; k < 5; k++)\r
- {\r
- int start = (i * 50) + (k * 10);\r
- int end = start + 10;\r
-\r
- if ( (end < s[j].getSequence().length) &&\r
- (start < s[j].getSequence().length))\r
- {\r
- out.append(s[j].getSequence(start, end));\r
-\r
- if (k < 4)\r
- {\r
- out.append(" ");\r
- }\r
- else\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- else\r
- {\r
- if (start < s[j].getSequence().length)\r
- {\r
- out.append(s[j].getSequenceAsString().substring(start));\r
- out.append("\n");\r
- }\r
- else\r
- {\r
- if (k == 0)\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- }\r
- }\r
-\r
- j++;\r
- }\r
-\r
- out.append("\n");\r
- }\r
-\r
- return out.toString();\r
- }\r
-}\r
+/*
+ * 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
+ * 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;
+
+/**
+ * <p>Title: </p>
+ * PileUpfile
+ * <p>Description: </p>
+ *
+ * Read and write PileUp style MSF Files.
+ * This used to be the MSFFile class, and was written according to the EBI's idea
+ * of a subset of the MSF alignment format. But, that was updated to reflect current
+ * GCG style IO fashion, as found in Emboss (thanks David Martin!)
+ *
+ **/
+import java.io.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+public class PileUpfile
+ extends MSFfile
+{
+
+ /**
+ * Creates a new MSFfile object.
+ */
+ public PileUpfile()
+ {
+ }
+
+ /**
+ * Creates a new MSFfile object.
+ *
+ * @param inFile DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public PileUpfile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+ public PileUpfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ public String print(SequenceI[] s)
+ {
+ StringBuffer out = new StringBuffer("PileUp\n\n");
+
+ int max = 0;
+ int maxid = 0;
+
+ int i = 0;
+ int bigChecksum = 0;
+ int[] checksums = new int[s.length];
+ while (i < s.length)
+ {
+ checksums[i] = checkSum(s[i].getSequenceAsString());
+ bigChecksum += checksums[i];
+ i++;
+ }
+
+ out.append(" MSF: " + s[0].getSequence().length +
+ " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n");
+
+ i = 0;
+ while ( (i < s.length) && (s[i] != null))
+ {
+ String seq = s[i].getSequenceAsString();
+ out.append(" Name: " + printId(s[i]) +
+ " oo Len: " +
+ seq.length() + " Check: " + checksums[i] +
+ " Weight: 1.00\n");
+
+ if (seq.length() > max)
+ {
+ max = seq.length();
+ }
+
+ if (s[i].getName().length() > maxid)
+ {
+ maxid = s[i].getName().length();
+ }
+
+ i++;
+ }
+
+ if (maxid < 10)
+ {
+ maxid = 10;
+ }
+
+ maxid++;
+ out.append("\n\n//\n\n");
+
+ int len = 50;
+
+ int nochunks = (max / len) + 1;
+
+ if ( (max % len) == 0)
+ {
+ nochunks--;
+ }
+
+ for (i = 0; i < nochunks; i++)
+ {
+ int j = 0;
+
+ while ( (j < s.length) && (s[j] != null))
+ {
+ String name = printId(s[j]);
+
+ out.append(new Format("%-" + maxid + "s").form(name + " "));
+
+ for (int k = 0; k < 5; k++)
+ {
+ int start = (i * 50) + (k * 10);
+ int end = start + 10;
+
+ if ( (end < s[j].getSequence().length) &&
+ (start < s[j].getSequence().length))
+ {
+ out.append(s[j].getSequence(start, end));
+
+ if (k < 4)
+ {
+ out.append(" ");
+ }
+ else
+ {
+ out.append("\n");
+ }
+ }
+ else
+ {
+ if (start < s[j].getSequence().length)
+ {
+ out.append(s[j].getSequenceAsString().substring(start));
+ out.append("\n");
+ }
+ else
+ {
+ if (k == 0)
+ {
+ out.append("\n");
+ }
+ }
+ }
+ }
+
+ j++;
+ }
+
+ out.append("\n");
+ }
+
+ return out.toString();
+ }
+}
{\r
super(inFile, type);\r
}\r
-\r
+ public StockholmFile(FileParse source) throws IOException\r
+ {\r
+ super(source);\r
+ }\r
public void initData()\r
{\r
super.initData();\r
// + ": " + seq);\r
this.seqs.addElement(seqO);\r
}\r
+ return; // finished parsing this segment of source\r
}\r
else if (!r.search(line))\r
{\r
git://source.jalview.org / jalview.git / commitdiff