X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=d84dc70801af742883d39b922e05d145cc7df9f2;hb=558597672640984d936ea22409a674293192a09c;hp=3a02041b10e733dba9d15ab00f4627286fb86a22;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 3a02041..d84dc70 100755 --- a/src/jalview/io/PfamFile.java +++ b/src/jalview/io/PfamFile.java @@ -1,49 +1,63 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 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.*; -public class PfamFile extends AlignFile { +import jalview.datamodel.*; +import jalview.util.*; - Vector ids; +public class PfamFile + extends AlignFile +{ public PfamFile() - {} - - public PfamFile(String inStr) { - super(inStr); + { } - public void initData() { - super.initData(); - ids = new Vector(); + public PfamFile(String inFile, String type) + throws IOException + { + super(inFile, type); } - public PfamFile(String inFile, String type) throws IOException { - super(inFile,type); + public void initData() + { + super.initData(); } - public void parse() throws IOException{ + public void parse() throws IOException + { int i = 0; String line; - Hashtable seqhash = new Hashtable(); - Vector headers = new Vector(); - - - while ((line = nextLine()) != null) - { + Vector headers = new Vector(); + while ( (line = nextLine()) != null) + { if (line.indexOf(" ") != 0) { if (line.indexOf("#") != 0) { - - StringTokenizer str = new StringTokenizer(line," "); + StringTokenizer str = new StringTokenizer(line, " "); String id = ""; if (str.hasMoreTokens()) @@ -53,16 +67,19 @@ public class PfamFile extends AlignFile { 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 = (StringBuffer) seqhash.get(id); + } + else + { + tempseq = new StringBuffer(); + seqhash.put(id, tempseq); + } + if (! (headers.contains(id))) + { + headers.addElement(id); + } tempseq.append(str.nextToken()); } @@ -71,67 +88,38 @@ public class PfamFile extends AlignFile { } 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(); - - String head = headers.elementAt(i).toString(); - int start = 1; - int end = seqhash.get(headers.elementAt(i)).toString().length(); - - if (head.indexOf("/") > 0 ) { - StringTokenizer st = new StringTokenizer(head,"/"); - if (st.countTokens() == 2) { - ids.addElement(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(); - } else - { - start = -1; - end = -1; - } - } else - ids.addElement(headers.elementAt(i)); - - } - else - ids.addElement(headers.elementAt(i)); + if (noSeqs < 1) + { + throw new IOException("No sequences found (PFAM input)"); + } - Sequence newSeq = null; - if (start != -1 && end != -1) - { - newSeq = new Sequence(ids.elementAt(i).toString(), - seqhash.get(headers.elementAt(i).toString()).toString(),start,end); - seqs.addElement(newSeq); - } - else + for (i = 0; i < headers.size(); i++) + { + if (seqhash.get(headers.elementAt(i)) != null) + { + if (maxLength < seqhash.get(headers.elementAt(i)).toString() + .length()) { - newSeq = new Sequence(ids.elementAt(i).toString(), - seqhash.get(headers.elementAt(i).toString()).toString(),1, - seqhash.get(headers.elementAt(i).toString()).toString().length()); - seqs.addElement(newSeq); + maxLength = seqhash.get(headers.elementAt(i)).toString() + .length(); } - if(!isValidProteinSequence(newSeq.getSequence())) - throw new IOException("Not a valid protein sequence - (PFAM input)"); - } - else - System.err.println("PFAM File reader: Can't find sequence for " + headers.elementAt(i)); + 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 static String print(SequenceI[] s) { + public String print(SequenceI[] s) + { StringBuffer out = new StringBuffer(""); int max = 0; @@ -139,35 +127,45 @@ public class PfamFile extends AlignFile { int i = 0; - while (i < s.length && s[i] != null) { - String tmp = s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd(); + while ( (i < s.length) && (s[i] != null)) + { + String tmp = printId(s[i]); - if (s[i].getSequence().length() > max) { - max = s[i].getSequence().length(); + if (s[i].getSequence().length > max) + { + max = s[i].getSequence().length; } - if (tmp.length() > maxid) { + + if (tmp.length() > maxid) + { maxid = tmp.length(); } + i++; } - if (maxid < 15) { + if (maxid < 15) + { maxid = 15; } int j = 0; - while ( j < s.length && s[j] != null) { - out.append( new Format("%-" + maxid + "s").form(s[j].getName() + "/" + s[j].getStart() + "-" + s[j].getEnd() ) + " "); - out.append(s[j].getSequence() + "\n"); + 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() { + public String print() + { return print(getSeqsAsArray()); } }