Kegg pathway diagrams (missing part 3)

Script

URL inputURL = null;
if (base != void) {
	inputURL = new URL(new URL(base), url);
} else {
	inputURL = new URL(url);
}

byte[] contents;
if (inputURL.openConnection().getContentLength() == -1) {
	// Content size unknown, must read first...
	byte[] buffer = new byte[1024];
	int bytesRead = 0;
	int totalBytesRead = 0;
	InputStream is = inputURL.openStream();
	while (bytesRead != -1) {
		totalBytesRead += bytesRead;
		bytesRead = is.read(buffer, 0, 1024);
	}
	contents = new byte[totalBytesRead];
} else {
	contents = new byte[inputURL.openConnection().getContentLength()];
}
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
while (bytesRead != -1) {
	bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
	totalBytesRead += bytesRead;
	if (contents.length==totalBytesRead) break;
}

image = contents;

Wsdl

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Wsdl

Wsdl Operation

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

Script

List bg_colors = new ArrayList();
List fg_colors = new ArrayList();
for (int i = 0; i < genes_list.size(); i++) {
	fg_colors.add(fg_color);
	bg_colors.add(bg_color);
}

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

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()) {
		String s = matcher.group(theGroup);
		s = s.trim();
		filteredlist.add(s);
	}
}

Value

Value

Script

ArrayList n = new ArrayList();
for (int i = 0; i < in0.size(); i++) {
	ArrayList tmp = new ArrayList();
	tmp.add (in0.get(i));
	n.add(tmp);
}

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

if (command == void || command.equals("")) {
	throw new RuntimeException("The 'command' port cannot be null.");
}
Process proc = null;
Runtime rt = Runtime.getRuntime();

String osName = System.getProperty("os.name");
String[] cmdArray = null;
if (osName.equals("Windows NT") || osName.equals("Windows XP")) {
	cmdArray = new String[] { "cmd.exe", "/c", command };
} else if (osName.equals("Windows 95")) {
	cmdArray = new String[] { "command.exe", "/c", command };
} else {// TODO: investigate if this will work in Linux and OSX
	cmdArray = new String[] { command };
}


// concatenate the arrays
if (args == null) {
	String args = new String();
}


int argSize = cmdArray.length + 1;
ArrayList appArray = new ArrayList(argSize);
for (int i = 0; i < cmdArray.length; i++) {
	appArray.add(cmdArray[i]);
}
appArray.add(args);

String[] applist = new String[argSize];
appArray.toArray(applist);

File f = new File("D:/blastdb/");
proc = rt.exec(applist,null,f);

// Get the input stream and read from it
InputStream in = proc.getInputStream();

int c;
StringBuffer sb = new StringBuffer();
while ((c = in.read()) != -1) {
	sb.append((char) c);
}
in.close();
result = sb.toString();

Value

Value

Script

BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

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]);
	}
}

Value

Script

import java.util.regex.*;

filteredlist = new ArrayList();
Pattern thePat1 = Pattern.compile(regex1);
Pattern thePat2 = Pattern.compile(regex2);
int theGroup = Integer.parseInt(group);

for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	
	Matcher matcher1 = thePat1.matcher(item);
	Matcher matcher2 = thePat2.matcher(item);

	if (matcher1.find()) {
		filteredlist.add("file=" + file + "\r");
	} else if (matcher2.find()) {
		filteredlist.add("file1=" + file2 + "\r");
	} else {
		filteredlist.add(item);
	}
}

Value

Value

Script

BufferedWriter out = new BufferedWriter(new FileWriter(outputFile));
out.write(filecontents);
out.close();
outputFile = filecontents;

Script

String output = new String();
output = stringlist.get(0);
for (i = 1; i < stringlist.size(); i++)
{
	output = output + "\n" + stringlist.get(i);
}

Value

Value

Script

String fileUrl1 = new String();
fileUrl1 = fileurl + "/output/mgcat.log";
BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl1);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl1);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

BufferedReader in = getReader(fileUrl1);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

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]);
	}
}

Value

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()) {
		String t = new String();
		t = matcher.group(theGroup);
		t = t.trim();
		filteredlist.add(t);
	}
}

Value

Value

Script

double a = Double.valueOf(seqSim);
double b = Double.valueOf(reqSim);

if (a >= b)
{
	cont = 1;
}
else
{
	cont = 0;
}

Script

import javax.swing.JOptionPane;

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

Value

Value

Value

Script

addClassPath("D:/Biojava/" + "biojava-1.7.1.jar");

import org.biojava.bio.Annotation;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.FeatureFilter;
import org.biojava.bio.seq.FeatureHolder;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.io.SeqIOTools;

  createDatabaseFASTAFile(String source) {
    String EMBLfile = base_dir + "/EMBL/" + source;
    String FASTAfile = base_dir + "/FASTA/"
        + source.substring(0, source.length() - 4) + ".fna";
    BufferedReader br = null;
    try {
      br = new BufferedReader(new FileReader(EMBLfile));
    } catch (FileNotFoundException e1) {
      e1.printStackTrace();
    }

    // read the EMBL File
    SequenceIterator sequences = SeqIOTools.readEmbl(br);
    // create an array list to hold protein sequences
    ArrayList proteinSeqs = new ArrayList();

    while (sequences.hasNext()) { // iterate through the EMBL files
      try {
        Sequence seq = sequences.nextSequence();
        FeatureFilter ff = new FeatureFilter.ByType("CDS");

        // get the filtered Features
        FeatureHolder fh = seq.filter(ff);

        // iterate over the Features in fh
        for (Iterator i = fh.features(); i.hasNext();) {
          Feature f = (Feature) i.next();

          Annotation a = f.getAnnotation();

          // take protein sequence from EMBL file after the
          // "/translation tag"
          String cds = ">gi|" + (String) a.getProperty("locus_tag")
              + "|sp|" + (String) a.getProperty("protein_id")
              + "\n" + (String) a.getProperty("translation")
              + "\n";

          // add elements to the array list
          proteinSeqs.add(cds);
        }
      } catch (BioException ex) { // not in EMBL format
        ex.printStackTrace();
        // request for more sequence when there isn't any
      } catch (NoSuchElementException ex) {
        ex.printStackTrace();
      }
    }

    FileWriter fstream;
    int j = -1;
    try {
      fstream = new FileWriter(FASTAfile);
      BufferedWriter out = new BufferedWriter(fstream);
      for (Iterator it = proteinSeqs.iterator(); it.hasNext();) {
        String s = (String) it.next();
        try {
          j++;
          out.write(s);
        } catch (Exception exc) {
          exc.printStackTrace();
        }
      }
      out.close();
      fstream.close();
    } catch (IOException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
  }

BufferedReader br = null;
// attribute holding the filename that will be converted to an fna file
// and then blast database
String database;
// attribute holding the filename that will be converted to multiple fna
// files
String target;
// filename for database fna output
String fno = base_dir + "/FASTA/"
		+ source_file_path.substring(0,
		source_file_path.length() - 4) + ".fna";

try {
	// *****
	createDatabaseFASTAFile(source_file_path);

	Runtime rt = Runtime.getRuntime();
	String runprog = progpath + "formatdb -i " + fno + " -n " 
			+ base_dir
			+ "/DATABASE/"
			+ source_file_path.substring(0, 
			source_file_path.length() - 4) + "_db";
	Process p = rt.exec(runprog);
} catch (IOException e) {
	e.getStackTrace();
}

database_dir = base_dir + "DATABASE/";