EBI_InterProScan for Taverna 2

Wsdl

Wsdl Operation

Script

import java.util.StringTokenizer;

interproscan_gff = "";

// Split into lines
StringTokenizer tok1 = new StringTokenizer(interproscan_text, "\n");
while(tok1.hasMoreElements()) {
  feat1 = tok1.nextElement();
  // Split into fields
  StringTokenizer tok2 = new StringTokenizer(feat1, "\t");
  fieldCount = 0;
  attributeStr = "";
  while(tok2.hasMoreElements()) {
    fieldCount++;
    fieldStr = tok2.nextElement();
    if(fieldCount < 2) { // First field is the ID
      interproscan_gff += fieldStr;
    }
    // The tool, feature, start and stop
    else if(fieldCount == 4 || (fieldCount > 5 && fieldCount < 9)) {
      interproscan_gff += "\t" + fieldStr;
    }
    // Score
    else if(fieldCount == 9) {
      if(fieldStr.equals("NA")) {
        interproscan_gff += "\t.";
      } else {
        interproscan_gff += "\t" + fieldStr;
      }
    }
    // Matching InterPro entry
    else if(fieldCount == 12 && !fieldStr.equals("NULL")) {
      attributeStr += fieldStr;
    }
    // Matching InterPro entry name
    else if(fieldCount == 13 && !fieldStr.equals("NULL")) {
      attributeStr += " " + fieldStr;
    }
  }
  interproscan_gff += "\t.\t.\tInterProScan";
  if(attributeStr.length() > 0) {
    interproscan_gff += " ; " + attributeStr;
  }
  interproscan_gff += "\n";
}

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Value

Value

Value

Value

Value

Value

Value

Wsdl

Wsdl Operation

Script

string = new String(bytes);

Script

string = new String(bytes);