From ca1259daa626e97eb62ee994addb6bd619360b64 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 19 Nov 2013 15:28:15 +0000
Subject: [PATCH] Remove internal FastaReader/FastaSequence and replace this
 with classes from JABAWS

---
 datadb/compbio/cassandra/CassandraWriter.java      |    1 +
 datadb/compbio/cassandra/FastaReader.java          |  173 -------------------
 datadb/compbio/cassandra/FastaSequence.java        |  179 --------------------
 datadb/compbio/cassandra/JpredParserHTTP.java      |    2 +
 datadb/compbio/cassandra/JpredParserLocalFile.java |    3 +
 engine/compbio/engine/JpredJob.java                |    2 +-
 6 files changed, 7 insertions(+), 353 deletions(-)
 delete mode 100644 datadb/compbio/cassandra/FastaReader.java
 delete mode 100644 datadb/compbio/cassandra/FastaSequence.java

diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java
index 48bbda7..24abd4b 100644
--- a/datadb/compbio/cassandra/CassandraWriter.java
+++ b/datadb/compbio/cassandra/CassandraWriter.java
@@ -8,6 +8,7 @@ import com.datastax.driver.core.Row;
 import com.datastax.driver.core.Session;
 import com.datastax.driver.core.ResultSet;
 
+import compbio.data.sequence.FastaSequence;
 import compbio.engine.JpredJob;
 import compbio.engine.ProteoCachePropertyHelperManager;
 import compbio.util.PropertyHelper;
diff --git a/datadb/compbio/cassandra/FastaReader.java b/datadb/compbio/cassandra/FastaReader.java
deleted file mode 100644
index 4783b14..0000000
--- a/datadb/compbio/cassandra/FastaReader.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package compbio.cassandra;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.InputStream;
-import java.util.Iterator;
-import java.util.Scanner;
-
-//import compbio.util.Util;
-
-/**
- * Reads files with FASTA formatted sequences. All the information in the FASTA
- * header is preserved including trailing white spaces. All the white spaces are
- * removed from the sequence.
- * 
- * Examples of the correct input:
- * 
- * <pre>
- * 
- * >zedpshvyzg
- * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
- * 
- * >xovkactesa
- * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
- * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
- * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
- * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
- * 
- * >ntazzewyvv
- * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
- * EASINM	AQQWRSLPPSRIMKLNG	HGCDCMHSHMEAD	DTKQSGIKGTFWNG	HDAQWLCRWG	
- * EFITEA	WWGRWGAITFFHAH	ENKNEIQECSDQNLKE	SRTTCEIID   TCHLFTRHLDGW 
- *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
- *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
- *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
- * 
- *    > 12 d t y wi 		k	jbke  	
- *   KLSHHDCD
- *    N
- *     H
- *     HSKCTEPHCGNSHQMLHRDP
- *     CCDQCQSWEAENWCASMRKAILF
- * 
- * </pre>
- * 
- * @author Peter Troshin
- * @version 1.0 April 2011
- * 
- */
-public class FastaReader implements Iterator<FastaSequence> {
-
-	private final Scanner input;
-	/**
-	 * Delimiter for the scanner
-	 */
-	private final String DELIM = ">";
-
-	/**
-	 * Header data can contain non-ASCII symbols and read in UTF8
-	 * 
-	 * @param inputFile
-	 *            the file containing the list of FASTA formatted sequences to
-	 *            read from
-	 * @throws FileNotFoundException
-	 *             if the input file is not found
-	 * @throws IllegalStateException
-	 *             if the close method was called on this instance
-	 * 
-	 */
-	public FastaReader(final String inputFile) throws FileNotFoundException {
-		input = new Scanner(new File(inputFile), "UTF8");
-		input.useDelimiter(DELIM);
-		Runtime.getRuntime().addShutdownHook(new Thread() {
-
-			@Override
-			public void run() {
-				if (input != null) {
-					input.close();
-				}
-			}
-		});
-	}
-
-	/**
-	 * This class will not close the incoming stream! So the client should do
-	 * so.
-	 * 
-	 * @param inputStream
-	 * @throws FileNotFoundException
-	 */
-	public FastaReader(final InputStream inputStream)
-			throws FileNotFoundException {
-		input = new Scanner(inputStream);
-		input.useDelimiter(DELIM);
-	}
-
-	/**
-	 * {@inheritDoc}
-	 * 
-	 * @throws IllegalStateException
-	 *             if the close method was called on this instance
-	 */
-	@Override
-	public boolean hasNext() {
-		return input.hasNext();
-	}
-
-	/**
-	 * Reads the next FastaSequence from the input
-	 * 
-	 * @throws AssertionError
-	 *             if the header or the sequence is missing
-	 * @throws IllegalStateException
-	 *             if the close method was called on this instance
-	 * @throws MismatchException
-	 *             - if there were no more FastaSequence's.
-	 */
-	@Override
-	public FastaSequence next() {
-		String fastaHeader = input.next();
-		while (fastaHeader.indexOf("\n") < 0 && input.hasNext()) {
-			fastaHeader = fastaHeader.concat(">");
-			fastaHeader = fastaHeader.concat(input.next());
-		}
-		return FastaReader.toFastaSequence(fastaHeader);
-	}
-
-	/**
-	 * Not implemented
-	 */
-	@Override
-	public void remove() {
-		throw new UnsupportedOperationException();
-	}
-
-	/**
-	 * Call this method to close the connection to the input file if you want to
-	 * free up the resources. The connection will be closed on the JVM shutdown
-	 * if this method was not called explicitly. No further reading on this
-	 * instance of the FastaReader will be possible after calling this method.
-	 */
-	public void close() {
-		input.close();
-	}
-
-	private static FastaSequence toFastaSequence(final String singleFastaEntry) {
-
-		// assert !Util.isEmpty(singleFastaEntry) :
-		// "Empty String where FASTA sequence is expected!";
-
-		int nlineidx = singleFastaEntry.indexOf("\n");
-		if (nlineidx < 0) {
-			throw new AssertionError(
-					"The FASTA sequence must contain the header information"
-							+ " separated by the new line from the sequence. Given sequence does not appear to "
-							+ "contain the header! Given data:\n "
-							+ singleFastaEntry);
-		}
-		String header = singleFastaEntry.substring(0, nlineidx);
-
-		// Get rid of the new line chars (should cover common cases)
-		header = header.replaceAll("\r", "");
-
-		String sequence = singleFastaEntry.substring(nlineidx);
-
-		/*
-		 * if (Util.isEmpty(sequence)) { throw new AssertionError(
-		 * "Empty sequences are not allowed! Please make sure the " +
-		 * " data is in the FASTA format! Given data:\n " + singleFastaEntry); }
-		 */
-		return new FastaSequence(header, sequence);
-	}
-}
diff --git a/datadb/compbio/cassandra/FastaSequence.java b/datadb/compbio/cassandra/FastaSequence.java
deleted file mode 100644
index 61f49c7..0000000
--- a/datadb/compbio/cassandra/FastaSequence.java
+++ /dev/null
@@ -1,179 +0,0 @@
-package compbio.cassandra;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-
-//import compbio.util.SysPrefs;
-//import compbio.util.annotation.Immutable;
-
-/**
- * A FASTA formatted sequence. Please note that this class does not make any
- * assumptions as to what sequence it stores e.g. it could be nucleotide,
- * protein or even gapped alignment sequence! The only guarantee it makes is
- * that the sequence does not contain white space characters e.g. spaces, new
- * lines etc
- * 
- * @author pvtroshin
- * 
- * @version 1.0 September 2009
- */
-
-@XmlAccessorType(XmlAccessType.FIELD)
-//@Immutable
-public class FastaSequence {
-
-	/**
-	 * Sequence id
-	 */
-	private String id;
-
-	// TODO what about gapped sequence here! should be indicated
-	/**
-	 * Returns the string representation of sequence
-	 */
-	private String sequence;
-
-	FastaSequence() {
-		// Default constructor for JaxB
-	}
-
-	/**
-	 * Upon construction the any whitespace characters are removed from the
-	 * sequence
-	 * 
-	 * @param id
-	 * @param sequence
-	 */
-	public FastaSequence(String id, String sequence) {
-		this.id = id;
-		this.sequence = sequence;
-	}
-
-	/**
-	 * Gets the value of id
-	 * 
-	 * @return the value of id
-	 */
-	public String getId() {
-		return this.id;
-	}
-
-	/**
-	 * Gets the value of sequence
-	 * 
-	 * @return the value of sequence
-	 */
-	public String getSequence() {
-		return this.sequence;
-	}
-
-	public static int countMatchesInSequence(final String theString,
-			final String theRegExp) {
-		final Pattern p = Pattern.compile(theRegExp);
-		final Matcher m = p.matcher(theString);
-		int cnt = 0;
-		while (m.find()) {
-			cnt++;
-		}
-		return cnt;
-	}
-
-	public String getFormattedFasta() {
-		return getFormatedSequence(80);
-	}
-
-	/**
-	 * 
-	 * @return one line name, next line sequence, no matter what the sequence
-	 *         length is
-	 */
-/*	public String getOnelineFasta() {
-		String fasta = ">" + getId() + SysPrefs.newlinechar;
-		fasta += getSequence() + SysPrefs.newlinechar;
-		return fasta;
-	}
-
-	/**
-	 * Format sequence per width letter in one string. Without spaces.
-	 * 
-	 * @return multiple line formated sequence, one line width letters length
-	 * 
-	 */
-	public String getFormatedSequence(final int width) {
-		if (sequence == null) {
-			return "";
-		}
-
-		assert width >= 0 : "Wrong width parameter ";
-
-		final StringBuilder sb = new StringBuilder(sequence);
-		// int tail = nrOfWindows % WIN_SIZE;
-		// final int turns = (nrOfWindows - tail) / WIN_SIZE;
-
-		int tailLen = sequence.length() % width;
-		// add up inserted new line chars
-		int nchunks = (sequence.length() - tailLen) / width;
-		int nlineCharcounter = 0;
-		int insPos = 0;
-		for (int i = 1; i <= nchunks; i++) {
-			insPos = width * i + nlineCharcounter;
-			// to prevent inserting new line in the very end of a sequence then
-			// it would have failed.
-			if (sb.length() <= insPos) {
-				break;
-			}
-			sb.insert(insPos, "\n");
-			nlineCharcounter++;
-		}
-		// sb.insert(insPos + tailLen, "\n");
-		return sb.toString();
-	}
-
-	/**
-	 * 
-	 * @return sequence length
-	 */
-	public int getLength() {
-		return this.sequence.length();
-	}
-
-	/**
-	 * Same as oneLineFasta
-	 */
-//	@Override
-//	public String toString() {
-//		return this.getOnelineFasta();
-	// }
-
-	@Override
-	public int hashCode() {
-		final int prime = 17;
-		int result = 1;
-		result = prime * result + ((id == null) ? 0 : id.hashCode());
-		result = prime * result
-				+ ((sequence == null) ? 0 : sequence.hashCode());
-		return result;
-	}
-
-	@Override
-	public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof FastaSequence)) {
-			return false;
-		}
-		FastaSequence fs = (FastaSequence) obj;
-		if (!fs.getId().equals(this.getId())) {
-			return false;
-		}
-		if (!fs.getSequence().equalsIgnoreCase(this.getSequence())) {
-			return false;
-		}
-		return true;
-	}
-
-}
diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index e53ddd8..2167a2d 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -15,6 +15,8 @@ import java.util.Date;
 import java.util.List;
 
 import compbio.cassandra.JpredParser;
+import compbio.data.sequence.FastaReader;
+import compbio.data.sequence.FastaSequence;
 import compbio.engine.JpredJob;
 
 public class JpredParserHTTP implements JpredParser {
diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index d4a22e6..f48178c 100644
--- a/datadb/compbio/cassandra/JpredParserLocalFile.java
+++ b/datadb/compbio/cassandra/JpredParserLocalFile.java
@@ -15,6 +15,9 @@ import java.util.Calendar;
 import java.util.Date;
 import java.util.List;
 
+import compbio.data.sequence.FastaReader;
+import compbio.data.sequence.FastaSequence;
+
 public class JpredParserLocalFile implements JpredParser {
 	private CassandraWriter cw = new CassandraWriter();
 	private String dirprefix;
diff --git a/engine/compbio/engine/JpredJob.java b/engine/compbio/engine/JpredJob.java
index a606746..db4a7fe 100644
--- a/engine/compbio/engine/JpredJob.java
+++ b/engine/compbio/engine/JpredJob.java
@@ -3,7 +3,7 @@ package compbio.engine;
 import java.util.ArrayList;
 import java.util.List;
 
-import compbio.cassandra.FastaSequence;
+import compbio.data.sequence.FastaSequence;
 
 public class JpredJob extends Job {
 	private String protein;
-- 
1.7.10.2