apollo.dataadapter.genbank
Class GenbankFormatter

java.lang.Object
  apollo.dataadapter.genbank.GenbankFormatter

public class GenbankFormatter
extends java.lang.Object

GenbankFormatter.java Created: Mon Sep 1 18:32:20 2003

Version:

1.0 $Header: /tmp/rob/gmod/gmod_cvs/apollo/src/java/apollo/dataadapter/genbank/GenbankFormatter.java,v 1.8 2004-06-23 00:00:01 nomi Exp $

Author:

Shiran Pasternak, Ryan Lozado

Constructor Summary

GenbankFormatter()

Method Summary

static java.lang.String	breakSingle(java.lang.String str) Formats a string so that it does not run beyond a specified line length.
static java.lang.String	breakSingle(java.lang.String str, int indent)
static java.lang.String	formatSequence(java.lang.String residues) Return GenBank-formatted sequence, e.g.
static java.lang.String	getFeature(java.lang.String feature)
static java.lang.String	getFeatureHeading(java.lang.String sub, java.lang.String info)
static java.lang.String	getFeatureItem(java.lang.String name, java.lang.String value)
static java.lang.String	getHeading(java.lang.String heading)
static java.lang.String	getSubHeading(java.lang.String sub)
static java.lang.String	padBetweenWithSpaces(java.lang.String str1, java.lang.String str2, int width) Pad with spaces between str1 and str2 to attain total width

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenbankFormatter

public GenbankFormatter()

Method Detail

padBetweenWithSpaces

public static java.lang.String padBetweenWithSpaces(java.lang.String str1,
                                                    java.lang.String str2,
                                                    int width)

Pad with spaces between str1 and str2 to attain total width

breakSingle

public static java.lang.String breakSingle(java.lang.String str)

Formats a string so that it does not run beyond a specified line length. if the string is longer than that, it is split up, and proper indentations are inserted to maintain the expected format.

Returns:

if longer than the line length, returns a multi-line, formatted string

breakSingle

public static java.lang.String breakSingle(java.lang.String str,
                                           int indent)

getHeading

public static java.lang.String getHeading(java.lang.String heading)

getSubHeading

public static java.lang.String getSubHeading(java.lang.String sub)

getFeature

public static java.lang.String getFeature(java.lang.String feature)

getFeatureHeading

public static java.lang.String getFeatureHeading(java.lang.String sub,
                                                 java.lang.String info)

getFeatureItem

public static java.lang.String getFeatureItem(java.lang.String name,
                                              java.lang.String value)

formatSequence

public static java.lang.String formatSequence(java.lang.String residues)

Return GenBank-formatted sequence, e.g. 1 GCTCCTAGGC ATCTGCCTAG TCACCCAAAT CATCACAGGC CTTCTCCTAG CTATGCACTA CACAGCAGAC 61 CACAGCAGAC ACCTCCCTAG CCTTCACCTC CGTAGCCCAC ACCTGCCGAA ACGTCCAATT CGGCTGACTC