/*
-* 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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 jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-
-public class PileUpfile
- extends AlignFile
+ * <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 jalview.datamodel.SequenceI;
+import jalview.util.Format;
+
+import java.io.IOException;
+
+public class PileUpfile extends MSFfile
{
-public PileUpfile()
-{}
-
-public PileUpfile(String inStr) {
- super(inStr);
-}
-
-public PileUpfile(String inFile, String type) throws IOException {
- super(inFile,type);
-}
-
-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 PileUpfile " + e);
- e.printStackTrace();
+ /**
+ * Creates a new MSFfile object.
+ */
+ public PileUpfile()
+ {
}
- this.noSeqs = headers.size();
+ /**
+ * 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);
+ }
- //Add sequences to the hash
- for (i = 0; i < headers.size(); i++ ) {
+ public PileUpfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
- if ( seqhash.get(headers.elementAt(i)) != null) {
- String head = headers.elementAt(i).toString();
- String seq = seqhash.get(head).toString();
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
- int start = 1;
- int end = seq.length();
+ public String print(SequenceI[] s)
+ {
+ StringBuffer out = new StringBuffer("PileUp");
+ out.append(newline);
+ out.append(newline);
+
+ 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++;
+ }
- if (maxLength < head.length() ) {
- maxLength = head.length();
+ out.append(" MSF: " + s[0].getSequence().length
+ + " Type: P Check: " + bigChecksum % 10000 + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
+
+ 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");
+ out.append(newline);
+
+ if (seq.length() > max)
+ {
+ max = seq.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();
- }
- }
+ if (s[i].getName().length() > maxid)
+ {
+ maxid = s[i].getName().length();
}
- Sequence newSeq = new Sequence(head,seq,start,end);
-
- seqs.addElement(newSeq);
-
- } else {
- System.err.println("PileUpfile Parser: Can't find sequence for " + headers.elementAt(i));
+ i++;
}
- }
-
-}
-
-public static int checkSum(String seq) {
- //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
- int check = 0;
-
- String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
- index += "--------------------------------------------------------------------------------------------------------------------------------";
- for(int i = 0; i < seq.length(); i++) {
- try {
- if (i <seq.length()) {
- int pos = index.indexOf(seq.substring(i,i+1));
- if (!index.substring(pos,pos+1).equals("_")) {
- check += ((i % 57) + 1) * pos;
- }
- }
- } catch (Exception e) {
- System.err.println("Exception during MSF Checksum calculation");
- e.printStackTrace();
+ if (maxid < 10)
+ {
+ maxid = 10;
}
- }
- return check % 10000;
-}
-public static String print(SequenceI[] s) {
- StringBuffer out = new StringBuffer("PileUp\n\n");
+ maxid++;
+ out.append(newline);
+ out.append(newline);
+ out.append("//");
+ out.append(newline);
+ out.append(newline);
- int max = 0;
- int maxid = 0;
+ int len = 50;
- int i = 0;
- String big = "";
- while (i < s.length && s[i] != null) {
- big += s[i].getSequence();
- i++;
- }
- i = 0;
- int bigcheck = checkSum(big);
-
- out.append(" MSF: " + s[0].getSequence().length() + " Type: P Check: " + bigcheck + " ..\n\n\n");
+ int nochunks = (max / len) + 1;
- while (i < s.length && s[i] != null) {
- String seq = s[i].getSequence();
- String name = s[i].getName()+ "/" + s[i].getStart() + "-" + s[i].getEnd();
- int check = checkSum(s[i].getSequence());
- out.append(" Name: " + name + " oo Len: " + s[i].getSequence().length() + " Check: " + check + " Weight: 1.00\n");
- if (seq.length() > max) {
- max = seq.length();
+ if ((max % len) == 0)
+ {
+ nochunks--;
}
- if (name.length() > maxid) {
- maxid = name.length();
- }
- i++;
- }
- if (maxid < 10) {
- maxid = 10;
- }
- maxid++;
- out.append( "\n\n//\n\n");
+ for (i = 0; i < nochunks; i++)
+ {
+ int j = 0;
- int len = 50;
+ while ((j < s.length) && (s[j] != null))
+ {
+ String name = printId(s[j]);
- 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++) {
+ 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 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 (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
- out.append(s[j].getSequence().substring(start,end));
- if (k < 4) {
- out.append(" ");
- } else {
- out.append("\n");
+ if (k < 4)
+ {
+ out.append(" ");
+ }
+ else
+ {
+ out.append(newline);
+ }
}
- } else {
- if (start < s[j].getSequence().length()) {
- out.append(s[j].getSequence().substring(start));
- out.append("\n");
- } else {
- if (k == 0) {
- out.append("\n");
+ else
+ {
+ if (start < s[j].getSequence().length)
+ {
+ out.append(s[j].getSequenceAsString().substring(start));
+ out.append(newline);
+ }
+ else
+ {
+ if (k == 0)
+ {
+ out.append(newline);
+ }
}
}
}
+
+ j++;
}
- j++;
+
+ out.append(newline);
}
- out.append("\n");
+ return out.toString();
}
- return out.toString();
-}
-public String print() {
- return print(getSeqsAsArray());
}
-}
-
-
-
-
-
-
-
git://source.jalview.org / jalview.git / blobdiff