Print Protein Information to HTML
Created: 2011-04-01 12:44:20
Takes in a lot of parameters in order to construct an HTML table to display the information.
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Workflow Components
Authors (0)
Titles (1)
| Print Protein Information to HTML |
Descriptions (1)
| Takes in a lot of parameters in order to construct an HTML table to display the information. |
Dependencies (0)
Inputs (12)
| Name |
Description |
| Write_Protein_HTML_GO |
Gene Ontology Information
|
| Write_Protein_HTML_input |
The location of the file where the HTML should be written.
|
| Write_Protein_HTML_InterPro |
The InterPro information
|
| Write_Protein_HTML_KDiagram |
The KEGG pathway diagram. Expected to be an image file.
|
| Write_Protein_HTML_KPI |
KEGG Pathway Information.
|
| Write_Protein_HTML_OC_R |
Any added Ondex concepts and relations.
|
| Write_Protein_HTML_PubMed |
PubMed references
|
| Write_Protein_HTML_Sid |
Source Protein IDs (from various sources)
|
| Write_Protein_HTML_SSpecies |
Source species name
|
| Write_Protein_HTML_Tid |
Target species IDS (variety)
|
| Write_Protein_HTML_Title |
The title of the table
|
| Write_Protein_HTML_TSpecies |
Target species name
|
Processors (2)
| Name |
Type |
Description |
| Write_Protein_HTML |
beanshell |
ScriptBufferedWriter out = new BufferedWriter(new FileWriter(input,true));
if (Title == void)
{Title = "";}
if (Tid == void)
{Tid = "";}
if (TSpecies == void)
{TSpecies = "";}
if (KPI == void)
{KPI = "";}
if (KDiagram == void)
{KDiagram = "";}
if (GO == void)
{GO = "";}
if (InterPro == void)
{InterPro = "";}
if (PubMed == void)
{PubMed = "";}
if (OC_R == void)
{OC_R = "";}
if (OS == void)
{OS = "";}
///////////////////////////////////////////////////////
out.write("
"+Title+"");
String [] lines = Tid.split("\n");
String output ="| Target Protein IDs | | | ";
for (String line: lines)
{
output += line+ "
";
}
output += " | ";
out.write(output);
if (TSpecies != void)
{
String [] lines = TSpecies.split("\n");
String output ="| Target Species | | ";
for (String line: lines)
{
output += " | " + line+ " | ";
}
out.write(output);
}
if (Sid != void)
{
String [] lines = Sid.split("\n");
String output ="| Source Protein IDs | | | ";
for (String line: lines)
{
output += line+ "
";
}
output+= " | ";
out.write(output);
}
if (SSpecies != void)
{
String [] lines = SSpecies.split("\n");
String output ="| Source Species | | ";
for (String line: lines)
{
output += " | " + line+ " | ";
}
out.write(output);
}
String [] lines = KPI.split("\n");
String output ="| KEGG Pathway Information | | ";
for (String line: lines)
{
output += " | " + line+ " | ";
}
out.write(output);
String [] lines = KDiagram.split("\n");
String output ="| KEGG Diagram | | ";
for (String line: lines)
{
output += " | ![](" + line+ ") | ";
}
out.write(output);
String [] lines = GO.split("\n");
String output ="| Gene Ontology Annotations | | | ";
for (String line: lines)
{
output += line+ "
";
}
output+= " | ";
out.write(output);
String [] lines = InterPro.split("\n");
String output ="| InterPro | | | ";
for (String line: lines)
{
output += line+ "
";
}
output+= " | ";
out.write(output);
String [] lines = PubMed.split("\n");
String output ="| Publications | | | ";
for (String line: lines)
{
output += line+ "
";
}
output+= " | ";
out.write(output);
String [] lines = OC_R.split("\n");
String output ="| New ONDEX Concepts and Relations | | | ";
for (String line: lines)
{
output += line+ "
";
}
output+= " | ";
out.write(output);
String [] lines = OS.split("\n");
String output ="| ONDEX Screenshots | | ";
for (String line: lines)
{
output += " | | ";
}
output+=" ";
out.write(output);
////////////////////////////////////////////
out.close();
output1 =input; |
| Read_Text_File |
localworker |
ScriptBufferedReader 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();
|
Beanshells (1)
| Name |
Description |
Inputs |
Outputs |
| Write_Protein_HTML |
|
Tid
TSpecies
Sid
SSpecies
KPI
input
KDiagram
GO
InterPro
PubMed
OC_R
Title
OS
|
file_path
|
Outputs (1)
| Name |
Description |
| HTML_filecontents |
|
Datalinks (14)
| Source |
Sink |
| Write_Protein_HTML_GO |
Write_Protein_HTML:GO |
| Write_Protein_HTML_input |
Write_Protein_HTML:input |
| Write_Protein_HTML_InterPro |
Write_Protein_HTML:InterPro |
| Write_Protein_HTML_KDiagram |
Write_Protein_HTML:KDiagram |
| Write_Protein_HTML_KPI |
Write_Protein_HTML:KPI |
| Write_Protein_HTML_OC_R |
Write_Protein_HTML:OC_R |
| Write_Protein_HTML_PubMed |
Write_Protein_HTML:PubMed |
| Write_Protein_HTML_Sid |
Write_Protein_HTML:Sid |
| Write_Protein_HTML_SSpecies |
Write_Protein_HTML:SSpecies |
| Write_Protein_HTML_Tid |
Write_Protein_HTML:Tid |
| Write_Protein_HTML_Title |
Write_Protein_HTML:Title |
| Write_Protein_HTML_TSpecies |
Write_Protein_HTML:TSpecies |
| Write_Protein_HTML:file_path |
Read_Text_File:fileurl |
| Read_Text_File:filecontents |
HTML_filecontents |
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licensed under:
Version 1
(of 1)
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