Compare two genomes for similarity

None

string = new String(bytes);

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

import java.util.regex.*;

filteredlist = new ArrayList();
Pattern thePat = Pattern.compile(regex);
int theGroup = Integer.parseInt(group);

for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	Matcher matcher = thePat.matcher(item);

	if (matcher.find()) {
		filteredlist.add(matcher.group(theGroup));
	}
}

import java.lang.Double;

double seqSimDbl = Double.valueOf(seqSim.trim()).doubleValue();
double minSimDbl = Double.valueOf(minSim.trim()).doubleValue();

int i = Double.compare(seqSimDbl,minSimDbl);

if (i >= 0)
{
	simBln = 1;
} else
{
	simBln = 0;
}
import javax.swing.JOptionPane;

answer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);

Name	Description
A_Sequence	Input the first sequence in FastA format
B_Sequence	Input the second sequence in FastA format

Name	Type	Description
needle	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/services/alignment_global.needle
Regex1	stringconstant	Value \n
Byte_Array_To_String	localworker	Script string = new String(bytes);
Split_string_into_string_list_by_regular_expression	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
Regex2	stringconstant	Value .*Similarity.+\((....)
Filter_list_of_strings_extracting_match_to_a_regex	localworker	Script import java.util.regex.*; filteredlist = new ArrayList(); Pattern thePat = Pattern.compile(regex); int theGroup = Integer.parseInt(group); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); Matcher matcher = thePat.matcher(item); if (matcher.find()) { filteredlist.add(matcher.group(theGroup)); } }
Group	stringconstant	Value 1
checkSimilarity	beanshell	Script import java.lang.Double; double seqSimDbl = Double.valueOf(seqSim.trim()).doubleValue(); double minSimDbl = Double.valueOf(minSim.trim()).doubleValue(); int i = Double.compare(seqSimDbl,minSimDbl); if (i >= 0) { simBln = 1; } else { simBln = 0; }
Ask	localworker	Script import javax.swing.JOptionPane; answer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);
message_value	stringconstant	Value Please enter the minimum percentage sequence similarity required
title_value	stringconstant	Value Sequence similarity

Source	Sink
A_Sequence	needle:asequence_direct_data
B_Sequence	needle:bsequence_direct_data
needle:outfile	Byte_Array_To_String:bytes
Regex1:value	Split_string_into_string_list_by_regular_expression:regex
Byte_Array_To_String:string	Split_string_into_string_list_by_regular_expression:string
Regex2:value	Filter_list_of_strings_extracting_match_to_a_regex:regex
Split_string_into_string_list_by_regular_expression:split	Filter_list_of_strings_extracting_match_to_a_regex:stringlist
Group:value	Filter_list_of_strings_extracting_match_to_a_regex:group
Filter_list_of_strings_extracting_match_to_a_regex:filteredlist	checkSimilarity:seqSim
Ask:answer	checkSimilarity:minSim
message_value:value	Ask:message
title_value:value	Ask:title
checkSimilarity:simBln	Carry_on

Compare two genomes for similarity

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