From c7d40b39964d85288d6ca965414d38d40cc1cbb2 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 18 Feb 2009 16:52:56 +0000
Subject: [PATCH] changes for test suite and put DNAPlotter panel in a
scrollpane
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9824 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../digest/CircularGenomeController.java | 28 ++++++++++++++-----
.../sanger/artemis/circular/digest/Utils.java | 11 ++++----
2 files changed, 27 insertions(+), 12 deletions(-)
diff --git a/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java b/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
index f7e854f25..a3b94a649 100644
--- a/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
+++ b/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
@@ -40,9 +40,11 @@ import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionAdapter;
import java.awt.event.MouseMotionListener;
import java.io.File;
+import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
+import java.util.Vector;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
@@ -63,10 +65,12 @@ public class CircularGenomeController
* Create in-silico PFGE from a restriction enzyme digest and draw
* alongside DNAPlotter
*/
- protected void setup(CircularGenomeCommandBean cgcb, String fileName) throws Exception
+ protected void setup(CircularGenomeCommandBean cgcb, List<String> fileNames)
+ throws Exception
{
try
{
+ String fileName = fileNames.get(0);
EntryGroup entryGroup = getEntryGroupFromFile(fileName);
if(fileName == null)
{
@@ -114,7 +118,8 @@ public class CircularGenomeController
}
p.waitFor();
- final ReportDetails rd = Utils.findCutSitesFromEmbossReport(output.getCanonicalPath());
+ final ReportDetails rd = Utils.findCutSitesFromEmbossReport(
+ new FileReader(output.getCanonicalPath()));
if (rd.cutSites.size() == 0)
JOptionPane.showMessageDialog(null,
@@ -173,8 +178,10 @@ public class CircularGenomeController
Dimension d = f.getToolkit().getScreenSize();
JPanel mainPanel = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ JScrollPane jspDNA = new JScrollPane(dna);
+
mainPanel.add(inSilicoGelPanel);
- mainPanel.add(dna);
+ mainPanel.add(jspDNA);
JScrollPane jsp = new JScrollPane(mainPanel);
jsp.getViewport().setBackground(Color.white);
@@ -288,21 +295,28 @@ public class CircularGenomeController
CircularGenomeController controller = new CircularGenomeController();
try
{
- String fileName = null;
+ List fileNames = null;
if(args != null && args.length > 0)
{
if(args.length == 1)
- fileName = args[0];
+ {
+ fileNames = new Vector();
+ fileNames.add(args[0]);
+ }
for(int i=0; i<args.length; i++)
{
if(args[i].startsWith("-enz"))
command.setEnzymeName(args[i+1]);
else if(args[i].startsWith("-seq"))
- fileName = args[i+1];
+ {
+ if(fileNames == null)
+ fileNames = new Vector();
+ fileNames.add(args[i+1]);
+ }
}
}
- controller.setup(command, fileName);
+ controller.setup(command, fileNames);
}
catch (Exception e)
{
diff --git a/uk/ac/sanger/artemis/circular/digest/Utils.java b/uk/ac/sanger/artemis/circular/digest/Utils.java
index fd19e72fd..fb4addab7 100644
--- a/uk/ac/sanger/artemis/circular/digest/Utils.java
+++ b/uk/ac/sanger/artemis/circular/digest/Utils.java
@@ -30,8 +30,8 @@ import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.sequence.MarkerRange;
import java.io.BufferedReader;
-import java.io.FileReader;
import java.io.IOException;
+import java.io.Reader;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
@@ -41,16 +41,17 @@ public class Utils
{
//private static final Logger logger = Logger.getLogger(Utils.class);
- public static ReportDetails findCutSitesFromEmbossReport(String fileName)
+ protected static ReportDetails findCutSitesFromEmbossReport(Reader reader)
{
EmbossTableParser etp = new EmbossTableParser();
ReportDetails ret = new ReportDetails();
try
{
- BufferedReader br = new BufferedReader(new FileReader(fileName));
+ BufferedReader br = new BufferedReader(reader);
ret.cutSites = etp.parse(br);
ret.length = etp.getLength();
- } catch (IOException exp)
+ }
+ catch (IOException exp)
{
throw new RuntimeException("Couldn't read, or parse results");
}
@@ -64,7 +65,7 @@ public class Utils
* @param entryGroup
* @return
*/
- public static DNADraw createDNADrawFromReportDetails(final ReportDetails rd,
+ protected static DNADraw createDNADrawFromReportDetails(final ReportDetails rd,
final EntryGroup entryGroup)
{
DNADraw dna = new DNADraw();
--
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