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Commit c7d40b39 authored by tjc's avatar tjc
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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
parent 257ed706
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......@@ -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)
{
......
......@@ -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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