X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=e954703ae153eb16c1b63273a48e0aba3afe9763;hb=08c7bee16c16563cc7cec7ea4d336b3e0c4c937a;hp=8e452e60ae2279fd752fca780897c08d93d36941;hpb=bacb105d85f7d068c8cd643cd337b832aeb80343;p=jalview.git
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 8e452e6..e954703 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,407 +1,414 @@
-/*
-* 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.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class MSFfile extends AlignFile
-{
- private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",
- "-");
- private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(
- "[" + jalview.util.Comparison.GapChars + "]", "\\~");
-
- /**
- * Creates a new MSFfile object.
- */
- public MSFfile()
- {
- }
-
- /**
- * Creates a new MSFfile object.
- *
- * @param inStr DOCUMENT ME!
- */
- public MSFfile(String inStr)
- {
- super(inStr);
- }
-
- /**
- * 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);
- }
-
- /**
- * DOCUMENT ME!
- */
- public void parse()
- {
- 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();
-
- int start = 1;
- int end = -1;
-
- if (maxLength < head.length())
- {
- maxLength = head.length();
- }
-
- if (head.indexOf("/") > 0)
- {
- StringTokenizer st = new StringTokenizer(head, "/");
-
- if (st.countTokens() == 2)
- {
- head = 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();
- }
- }
- }
-
- // Replace ~ with a sensible gap character
- seq = gapre.replaceAll(seq);
-
- Sequence newSeq = new Sequence(head, seq, start, end);
-
- 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 static int checkSum(String seq)
- {
- //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
- int check = 0;
- String sequence = seq.toUpperCase();
-
- String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
- index += "--------------------------------------------------------------------------------------------------------------------------------";
-
- for (int i = 0; i < sequence.length(); i++)
- {
- try
- {
- int pos = index.indexOf(sequence.charAt(i));
-
- if (index.charAt(pos)!='_')
- {
- check += (((i % 57) + 1) * pos);
- }
- }
- catch (Exception e)
- {
- System.err.println("Exception during MSF Checksum calculation");
- e.printStackTrace();
- }
- }
-
- return check % 10000;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static String print(SequenceI[] s)
- {
- return print(s, false);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param is_NA DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static String print(SequenceI[] s, boolean is_NA)
- {
- 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;
- String big = "";
-
- while ((i < s.length) && (s[i] != null))
- {
- String sq;
- big += (sq = s[i].getSequence());
-
- if (sq.length() > max)
- {
- max = sq.length();
- }
-
- i++;
- }
-
- Format maxLenpad = new Format("%" + (new String("" + max)).length() +
- "d");
- Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
- "d");
- i = 0;
-
- long bigcheck = checkSum(big);
- long maxNB = 0;
- out.append(" MSF: " + s[0].getSequence().length() + " Type: " +
- (is_NA ? "N" : "P") + " Check: " + bigcheck + " ..\n\n\n");
-
- String[] nameBlock = new String[s.length];
- String[] idBlock = new String[s.length];
-
- while ((i < s.length) && (s[i] != null))
- {
- String name = s[i].getName() + "/" + s[i].getStart() + "-" +
- s[i].getEnd();
- int check = checkSum(s[i].getSequence());
- nameBlock[i] = new String(" Name: " + name + " ");
- idBlock[i] = new String("Len: " +
- maxLenpad.form(s[i].getSequence().length()) + " Check:" +
- maxChkpad.form(check) + " Weight: 1.00\n");
-
- if (name.length() > maxid)
- {
- maxid = name.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 = s[j].getName();
- out.append(new Format("%-" + maxid + "s").form(name + "/" +
- s[j].getStart() + "-" + s[j].getEnd()) + " ");
-
- 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(re2gap.replaceAll(s[j].getSequence()
- .substring(start, end)));
-
- if (k < 4)
- {
- // out.append(" ");
- }
- else
- {
- out.append("\n");
- }
- }
- else
- {
- if (start < s[j].getSequence().length())
- {
- out.append(re2gap.replaceAll(
- s[j].getSequence().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());
- }
-}
+/*
+ * 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 java.util.Locale;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+import jalview.util.Format;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+
+/**
+ * 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, DataSourceType type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public MSFfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Read and parse MSF sequence data
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ boolean seqFlag = false;
+ List headers = new ArrayList();
+ Hashtable seqhash = new Hashtable();
+
+ try
+ {
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ StringTokenizer str = new StringTokenizer(line);
+
+ String key = null;
+ 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.add(key);
+ }
+
+ // if line has // set SeqFlag 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)
+ {
+ // sequence id is the first field
+ key = inStr;
+
+ StringBuilder tempseq;
+
+ // Get sequence from hash if it exists
+ if (seqhash.containsKey(key))
+ {
+ tempseq = seqhash.get(key);
+ }
+ else
+ {
+ tempseq = new StringBuilder(64);
+ seqhash.put(key, tempseq);
+ }
+
+ // loop through the rest of the words
+ while (str.hasMoreTokens())
+ {
+ // append the word to the sequence
+ String sequenceBlock = str.nextToken();
+ tempseq.append(sequenceBlock);
+ }
+ }
+ }
+ }
+ } catch (IOException e)
+ {
+ System.err.println("Exception parsing MSFFile " + e);
+ e.printStackTrace();
+ }
+
+ this.noSeqs = headers.size();
+
+ // Add sequences to the hash
+ for (int i = 0; i < headers.size(); i++)
+ {
+ if (seqhash.get(headers.get(i)) != null)
+ {
+ String head = headers.get(i);
+ String seq = seqhash.get(head).toString();
+
+ if (maxLength < head.length())
+ {
+ maxLength = head.length();
+ }
+
+ /*
+ * replace ~ (leading/trailing positions) with the gap character;
+ * use '.' as this is the internal gap character required by MSF
+ */
+ 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.get(i));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int checkSum(String seq)
+ {
+ int check = 0;
+ String sequence = seq.toUpperCase(Locale.ROOT);
+
+ 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!
+ */
+ @Override
+ public String print(SequenceI[] sqs, boolean jvSuffix)
+ {
+
+ boolean is_NA = Comparison.isNucleotide(sqs);
+
+ SequenceI[] s = new SequenceI[sqs.length];
+
+ StringBuilder out = new StringBuilder(256);
+ out.append("!!").append(is_NA ? "NA" : "AA")
+ .append("_MULTIPLE_ALIGNMENT 1.0");
+ // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+ out.append(newline);
+ out.append(newline);
+ int max = 0;
+ int maxid = 0;
+ int i = 0;
+
+ while ((i < sqs.length) && (sqs[i] != null))
+ {
+ /*
+ * modify to MSF format: uses '.' for internal gaps,
+ * and '~' for leading or trailing gaps
+ */
+ String seqString = sqs[i].getSequenceAsString().replace('-', '.');
+
+ StringBuilder sb = new StringBuilder(seqString);
+
+ 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] = new Sequence(sqs[i].getName(), sb.toString(),
+ sqs[i].getStart(), sqs[i].getEnd());
+
+ if (sb.length() > max)
+ {
+ max = sb.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].getLength() + " Type: "
+ + (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000)
+ + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
+
+ 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], jvSuffix) + " ");
+
+ idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getLength())
+ + " Check: " + maxChkpad.form(checksums[i])
+ + " Weight: 1.00" + newline);
+
+ 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(newline);
+ out.append(newline);
+ out.append("//");
+ out.append(newline);
+ out.append(newline);
+ int len = 50;
+
+ 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))
+ {
+ String name = printId(s[j], jvSuffix);
+
+ 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;
+
+ int length = s[j].getLength();
+ if ((end < length)
+ && (start < length))
+ {
+ out.append(s[j].getSequence(start, end));
+
+ if (k < 4)
+ {
+ out.append(" ");
+ }
+ else
+ {
+ out.append(newline);
+ }
+ }
+ else
+ {
+ if (start < length)
+ {
+ out.append(s[j].getSequenceAsString().substring(start));
+ out.append(newline);
+ }
+ else
+ {
+ if (k == 0)
+ {
+ out.append(newline);
+ }
+ }
+ }
+ }
+
+ j++;
+ }
+
+ out.append(newline);
+ }
+
+ return out.toString();
+ }
+}