-/*
- * Created on 17-May-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package uk.ac.vamsas.objects.utils;
-
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.util.regex.Pattern;
-
-import uk.ac.vamsas.objects.core.AlignmentSequence;
-import uk.ac.vamsas.objects.core.Sequence;
-import uk.ac.vamsas.objects.core.SequenceType;
-
-/**
- * @author jimp
- *
- * TODO To change the template for this generated type comment go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-public class Seq {
-
- public static void write_PirSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
- BufferedWriter pir_out = new BufferedWriter(new OutputStreamWriter(os));
- pir_out.write(">P1;"+seq.getName()+"\n");
- int width = (wid<1) ? 80 : wid;
- for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
- if (j+width<k)
- pir_out.write(seq.getSequence().substring(j,j+width)+"\n");
- else
- pir_out.write(seq.getSequence().substring(j)+"\n");
- pir_out.flush();
- }
-
- public static void write_FastaSeq(OutputStream os, SequenceType seq) throws IOException {
- BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
- fasta_out.write(">"+seq.getName()+"\n");
- fasta_out.write(seq.getSequence()+"\n");
- fasta_out.flush();
- }
-
- public static void write_FastaSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
- BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
- fasta_out.write(">"+seq.getName()+"\n");
- int width = (wid<1) ? 80 : wid;
- for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
- if (j+width<k)
- fasta_out.write(seq.getSequence().substring(j,j+width)+"\n");
- else
- fasta_out.write(seq.getSequence().substring(j)+"\n");
- fasta_out.flush();
- }
- /**
- *validate a SequenceType Vobject as an info:iubmb.org/aminoacid SequenceType
- *This version resolves references to Sequence objects from AlignmentSequence
- *TODO: Define info: urn for dictionary string (could also be regex of valid characters!)
- * @param s
- * @param dict TODO
- * @return true if a valid amino acid sequence Vobject
- */
- private static boolean valid_aadictionary_string(String s, String dict) {
- if (s==null)
- return false;
- // validate against dictionary
- // TODO generalise to resolve dictionary against info: urn for dictionary type
- Pattern aa_repl = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUX]+", Pattern.CASE_INSENSITIVE);
- String remnants = aa_repl.matcher(s).replaceAll("");
- return !remnants.matches("//S+");
- }
-
- public static Sequence newSequence(String Name, String Sequence, String Dictionary, int start, int end) {
- //TODO: make hierarchy reflecting the SeqType Vobject.
- Sequence seq= new Sequence();
- seq.setDictionary(Dictionary);
- seq.setName(Name);
- seq.setSequence(Sequence);
- seq.setStart(start);
- if (start<=end) {
- if ((end-start)!=Sequence.length())
- seq.setEnd(start+Sequence.length());
- } else {
- // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence Vobject
- if ((start-end)!=Sequence.length())
- seq.setEnd(end+Sequence.length());
- }
- return seq;
- }
- public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, long start, long end) {
- if (refseq!=null) {
- AlignmentSequence asq = new AlignmentSequence();
- asq.setName(name);
- asq.setSequence(alSequence);
- asq.setRefid(refseq);
- if (end>refseq.getEnd() || end<start || end==-1)
- end = refseq.getEnd();
- asq.setEnd(end);
- if (start<refseq.getStart())
- start = refseq.getStart();
- asq.setStart(start);
- return asq;
- }
- return null;
- }
- public static boolean is_valid_aa_seq(SequenceType s) {
- Sequence q;
- boolean validref=false;
- if (s instanceof Sequence) {
- q=(Sequence) s;
- if (q.getDictionary()!=null
-
- && q.getDictionary().length()>0
- || !q.getDictionary().equals(SymbolDictionary.STANDARD_AA))
- return false;
- return valid_aadictionary_string(q.getSequence(), SymbolDictionary.STANDARD_AA);
- }
-
- // follow references
- if (s instanceof AlignmentSequence) {
- Object w = (((AlignmentSequence) s).getRefid());
- if (w!=null && w!=s && w instanceof SequenceType)
- return is_valid_aa_seq((SequenceType) w)
- && valid_aadictionary_string(((AlignmentSequence) s).getSequence(), SymbolDictionary.STANDARD_AA);
- }
-
- return false;
- }
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client 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 Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.objects.utils;\r
+\r
+import java.io.BufferedWriter;\r
+import java.io.IOException;\r
+import java.io.OutputStream;\r
+import java.io.OutputStreamWriter;\r
+import java.util.regex.Pattern;\r
+\r
+import uk.ac.vamsas.objects.core.AlignmentSequence;\r
+import uk.ac.vamsas.objects.core.Sequence;\r
+import uk.ac.vamsas.objects.core.SequenceType;\r
+\r
+/**\r
+ * @author jimp\r
+ * \r
+ * TODO To change the template for this generated type comment go to\r
+ * Window - Preferences - Java - Code Style - Code Templates\r
+ */\r
+public class Seq {\r
+\r
+ public static void write_PirSeq(OutputStream os, SequenceType seq, int wid)\r
+ throws IOException {\r
+ BufferedWriter pir_out = new BufferedWriter(new OutputStreamWriter(os));\r
+ pir_out.write(">P1;" + seq.getName() + "\n");\r
+ int width = (wid < 1) ? 80 : wid;\r
+ for (int j = 0, k = seq.getSequence().length(); j < k; j += width)\r
+ if (j + width < k)\r
+ pir_out.write(seq.getSequence().substring(j, j + width) + "\n");\r
+ else\r
+ pir_out.write(seq.getSequence().substring(j) + "\n");\r
+ pir_out.flush();\r
+ }\r
+\r
+ public static void write_FastaSeq(OutputStream os, SequenceType seq)\r
+ throws IOException {\r
+ BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));\r
+ fasta_out.write(">" + seq.getName() + "\n");\r
+ fasta_out.write(seq.getSequence() + "\n");\r
+ fasta_out.flush();\r
+ }\r
+\r
+ public static void write_FastaSeq(OutputStream os, SequenceType seq, int wid)\r
+ throws IOException {\r
+ BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));\r
+ fasta_out.write(">" + seq.getName() + "\n");\r
+ int width = (wid < 1) ? 80 : wid;\r
+ for (int j = 0, k = seq.getSequence().length(); j < k; j += width)\r
+ if (j + width < k)\r
+ fasta_out.write(seq.getSequence().substring(j, j + width) + "\n");\r
+ else\r
+ fasta_out.write(seq.getSequence().substring(j) + "\n");\r
+ fasta_out.flush();\r
+ }\r
+\r
+ /**\r
+ *validate a SequenceType Vobject as an info:iubmb.org/aminoacid SequenceType\r
+ * This version resolves references to Sequence objects from AlignmentSequence\r
+ * TODO: Define info: urn for dictionary string (could also be regex of valid\r
+ * characters!)\r
+ * \r
+ * @param s\r
+ * @param dict\r
+ * TODO\r
+ * @return true if a valid amino acid sequence Vobject\r
+ */\r
+ private static boolean valid_aadictionary_string(String s, String dict) {\r
+ if (s == null)\r
+ return false;\r
+ // validate against dictionary\r
+ // TODO generalise to resolve dictionary against info: urn for dictionary\r
+ // type\r
+ Pattern aa_repl = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUX]+",\r
+ Pattern.CASE_INSENSITIVE);\r
+ String remnants = aa_repl.matcher(s).replaceAll("");\r
+ return !remnants.matches("//S+");\r
+ }\r
+\r
+ public static Sequence newSequence(String Name, String Sequence,\r
+ String Dictionary, int start, int end) {\r
+ // TODO: make hierarchy reflecting the SeqType Vobject.\r
+ Sequence seq = new Sequence();\r
+ seq.setDictionary(Dictionary);\r
+ seq.setName(Name);\r
+ seq.setSequence(Sequence);\r
+ seq.setStart(start);\r
+ if (start <= end) {\r
+ if ((end - start) != Sequence.length())\r
+ seq.setEnd(start + Sequence.length());\r
+ } else {\r
+ // reverse topology mapping. TODO: VAMSAS: decide if allowed to do\r
+ // start>end on Sequence Vobject\r
+ if ((start - end) != Sequence.length())\r
+ seq.setEnd(end + Sequence.length());\r
+ }\r
+ return seq;\r
+ }\r
+\r
+ public static AlignmentSequence newAlignmentSequence(String name,\r
+ String alSequence, Sequence refseq, long start, long end) {\r
+ if (refseq != null) {\r
+ AlignmentSequence asq = new AlignmentSequence();\r
+ asq.setName(name);\r
+ asq.setSequence(alSequence);\r
+ asq.setRefid(refseq);\r
+ if (end > refseq.getEnd() || end < start || end == -1)\r
+ end = refseq.getEnd();\r
+ asq.setEnd(end);\r
+ if (start < refseq.getStart())\r
+ start = refseq.getStart();\r
+ asq.setStart(start);\r
+ return asq;\r
+ }\r
+ return null;\r
+ }\r
+\r
+ public static boolean is_valid_aa_seq(SequenceType s) {\r
+ Sequence q;\r
+ boolean validref = false;\r
+ if (s instanceof Sequence) {\r
+ q = (Sequence) s;\r
+ if (q.getDictionary() != null\r
+\r
+ && q.getDictionary().length() > 0\r
+ || !q.getDictionary().equals(SymbolDictionary.STANDARD_AA))\r
+ return false;\r
+ return valid_aadictionary_string(q.getSequence(),\r
+ SymbolDictionary.STANDARD_AA);\r
+ }\r
+\r
+ // follow references\r
+ if (s instanceof AlignmentSequence) {\r
+ Object w = (((AlignmentSequence) s).getRefid());\r
+ if (w != null && w != s && w instanceof SequenceType)\r
+ return is_valid_aa_seq((SequenceType) w)\r
+ && valid_aadictionary_string(((AlignmentSequence) s).getSequence(),\r
+ SymbolDictionary.STANDARD_AA);\r
+ }\r
+\r
+ return false;\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff