From 8d3feacb69f915fe099654d80fba6b48d049f7dd Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 21 Apr 2009 13:09:32 +0000
Subject: [PATCH] allow restict output to be provided as an argument
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10569 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../digest/CircularGenomeController.java | 59 +++++++++++++++----
1 file changed, 49 insertions(+), 10 deletions(-)
diff --git a/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java b/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
index 7be4a0034..8171a2e54 100644
--- a/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
+++ b/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
@@ -86,8 +86,14 @@ public class CircularGenomeController
/**
* Create in-silico Pulse Field Gel Electrophoresis from a restriction enzyme
* digest and draw alongside DNAPlotter
+ * @param enzymes
+ * @param sequenceFiles
+ * @param restrictOutputs
+ * @throws Exception
*/
- protected void setup(String enzymes, List<File> sequenceFiles)
+ protected void setup(String enzymes,
+ List<File> sequenceFiles,
+ List<File> restrictOutputs)
throws Exception
{
// add each sequence file to a different entry group
@@ -114,14 +120,18 @@ public class CircularGenomeController
enzymes = promptForEnzymes();
// run restrict
- List<File> restrictOutputs = new Vector<File>(sequenceFiles.size());
- for (int i = 0; i < sequenceFiles.size(); i++)
+ if(restrictOutputs == null)
{
- File sequenceFile = sequenceFiles.get(i);
- File restrictOutput = File.createTempFile("restrict_"
- + sequenceFile.getName(), ".txt");
- restrictOutputs.add(restrictOutput);
- runEmbossRestrict(sequenceFile.getAbsolutePath(), enzymes, restrictOutput);
+ restrictOutputs = new Vector<File>(sequenceFiles.size());
+ for (int i = 0; i < sequenceFiles.size(); i++)
+ {
+ File sequenceFile = sequenceFiles.get(i);
+ File restrictOutput = File.createTempFile("restrict_"
+ + sequenceFile.getName(), ".txt");
+ restrictOutputs.add(restrictOutput);
+ runEmbossRestrict(sequenceFile.getAbsolutePath(), enzymes,
+ restrictOutput);
+ }
}
drawResults(restrictOutputs, entries, sequenceFiles, enzymes);
}
@@ -578,10 +588,21 @@ public class CircularGenomeController
try
{
List<File> fileNames = null;
+ List<File> restrictOutputs = null;
if (args != null && args.length > 0)
{
if (args.length == 1)
{
+ if(args[0].startsWith("-h"))
+ {
+ System.out.println("-h\t\tshow help");
+ System.out.println("-enz\t\tcomma separated list of digest enzymes (optional)");
+ System.out.println("-seq\t\tspace separated list of sequences (optional)");
+ System.out.println(
+ "-restrict\tspace separated lists of EMBOSS restrict output "+
+ "in the same order as the sequences (optional).");
+ System.exit(0);
+ }
fileNames = new Vector<File>();
fileNames.add(new File(args[0]));
}
@@ -594,11 +615,29 @@ public class CircularGenomeController
{
if (fileNames == null)
fileNames = new Vector<File>();
- fileNames.add(new File(args[i + 1]));
+
+ for(int j = i + 1; j < args.length; j++)
+ {
+ if(args[j].startsWith("-"))
+ break;
+ fileNames.add(new File(args[j]));
+ }
+ }
+ else if (args[i].startsWith("-restrict"))
+ {
+ if (restrictOutputs == null)
+ restrictOutputs = new Vector<File>();
+
+ for(int j = i + 1; j < args.length; j++)
+ {
+ if(args[j].startsWith("-"))
+ break;
+ restrictOutputs.add(new File(args[j]));
+ }
}
}
}
- controller.setup(enzymes, fileNames);
+ controller.setup(enzymes, fileNames, restrictOutputs);
}
catch (Exception e)
{
--
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