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package jalview.ws.jws2; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentView; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.Desktop; |
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import jalview.gui.JvOptionPane; |
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import jalview.gui.JvSwingUtils; |
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import jalview.util.MessageManager; |
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import jalview.ws.jws2.jabaws2.Jws2Instance; |
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import jalview.ws.params.WsParamSetI; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.awt.event.MouseAdapter; |
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import java.awt.event.MouseEvent; |
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import java.util.List; |
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import javax.swing.JMenu; |
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import javax.swing.JMenuItem; |
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import javax.swing.ToolTipManager; |
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import compbio.data.msa.MsaWS; |
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import compbio.metadata.Argument; |
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@author |
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@version |
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| 44.9% |
Uncovered Elements: 81 (147) |
Complexity: 39 |
Complexity Density: 0.42 |
|
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public class MsaWSClient extends Jws2Client |
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{ |
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MsaWS server; |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public MsaWSClient(Jws2Instance sh, String altitle,... |
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jalview.datamodel.AlignmentView msa, boolean submitGaps, |
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boolean preserveOrder, AlignmentI seqdataset, |
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AlignFrame _alignFrame) |
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{ |
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this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder, |
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seqdataset, _alignFrame); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,... |
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jalview.datamodel.AlignmentView msa, boolean submitGaps, |
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boolean preserveOrder, AlignmentI seqdataset, |
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AlignFrame _alignFrame) |
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{ |
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this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder, |
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seqdataset, _alignFrame); |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 17 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
|
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public MsaWSClient(Jws2Instance sh, WsParamSetI preset,... |
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List<Argument> arguments, boolean editParams, String altitle, |
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jalview.datamodel.AlignmentView msa, boolean submitGaps, |
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boolean preserveOrder, AlignmentI seqdataset, |
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AlignFrame _alignFrame) |
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{ |
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super(_alignFrame, preset, arguments); |
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if (!processParams(sh, editParams)) |
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{ |
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return; |
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} |
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if (!(sh.service instanceof MsaWS)) |
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{ |
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JvOptionPane.showMessageDialog(Desktop.desktop, |
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MessageManager.formatMessage( |
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"label.service_called_is_not_msa_service", |
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new String[] |
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{ sh.serviceType }), |
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MessageManager.getString("label.internal_jalview_error"), |
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JvOptionPane.WARNING_MESSAGE); |
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return; |
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} |
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server = (MsaWS) sh.service; |
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if ((wsInfo = setWebService(sh, false)) == null) |
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{ |
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JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager |
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.formatMessage("label.msa_service_is_unknown", new String[] |
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{ sh.serviceType }), |
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MessageManager.getString("label.internal_jalview_error"), |
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JvOptionPane.WARNING_MESSAGE); |
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return; |
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} |
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startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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3736 |
public MsaWSClient()... |
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{ |
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3736 |
super(); |
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} |
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| 0% |
Uncovered Elements: 25 (25) |
Complexity: 8 |
Complexity Density: 0.53 |
|
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0 |
private void startMsaWSClient(String altitle, AlignmentView msa,... |
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boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset) |
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{ |
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wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") |
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+ " of " + altitle + "\nJob details\n"); |
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String jobtitle = WebServiceName.toLowerCase(); |
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if (jobtitle.endsWith("alignment")) |
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{ |
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if (submitGaps && (!jobtitle.endsWith("realignment") |
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|| jobtitle.indexOf("profile") == -1)) |
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{ |
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int pos = jobtitle.indexOf("alignment"); |
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jobtitle = WebServiceName.substring(0, pos) + "re-alignment of " |
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+ altitle; |
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} |
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else |
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{ |
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jobtitle = WebServiceName + " of " + altitle; |
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} |
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} |
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else |
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{ |
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jobtitle = WebServiceName + (submitGaps ? " re" : " ") |
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+ "alignment of " + altitle; |
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} |
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MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, |
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wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps, |
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preserveOrder, seqdataset); |
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if (msathread.hasValidInput()) |
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{ |
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wsInfo.setthisService(msathread); |
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wsInfo.setVisible(true); |
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msathread.start(); |
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} |
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else |
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{ |
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wsInfo.setVisible(false); |
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JvOptionPane.showMessageDialog(alignFrame, |
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MessageManager.getString("info.invalid_msa_input_mininfo"), |
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MessageManager.getString("info.invalid_msa_notenough"), |
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JvOptionPane.INFORMATION_MESSAGE); |
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} |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public static void main(String[] args)... |
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{ |
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System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*")); |
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} |
196 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
197 |
0 |
protected String getServiceActionKey()... |
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{ |
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return "MsaWS"; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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protected String getServiceActionDescription()... |
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{ |
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return "Multiple Sequence Alignment"; |
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} |
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209 |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
213 |
7472 |
private boolean canSubmitGaps()... |
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{ |
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7472 |
return (WebServiceName.indexOf("lustal") > -1); |
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} |
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| 92.4% |
Uncovered Elements: 5 (66) |
Complexity: 12 |
Complexity Density: 0.25 |
|
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3736 |
@Override... |
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public void attachWSMenuEntry(JMenu rmsawsmenu, |
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final Jws2Instance service, final AlignFrame alignFrame) |
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{ |
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3736 |
if (registerAAConWSInstance(rmsawsmenu, service, alignFrame)) |
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{ |
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return; |
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} |
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3736 |
setWebService(service, true); |
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3736 |
boolean finished = true, submitGaps = false; |
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3736 |
JMenu msawsmenu = rmsawsmenu; |
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String svcname = WebServiceName; |
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if (svcname.endsWith("WS")) |
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{ |
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svcname = svcname.substring(0, svcname.length() - 2); |
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} |
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String calcName = svcname + " "; |
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if (canSubmitGaps()) |
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{ |
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msawsmenu = new JMenu(svcname); |
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rmsawsmenu.add(msawsmenu); |
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calcName = ""; |
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} |
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boolean hasparams = service.hasParameters(); |
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do |
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{ |
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4668 |
String action = "Align "; |
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4668 |
if (submitGaps == true) |
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{ |
250 |
932 |
action = "Realign "; |
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932 |
msawsmenu = new JMenu(MessageManager |
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.formatMessage("label.realign_with_params", new String[] |
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{ svcname })); |
254 |
932 |
msawsmenu.setToolTipText(MessageManager |
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.getString("label.align_sequences_to_existing_alignment")); |
256 |
932 |
rmsawsmenu.add(msawsmenu); |
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} |
258 |
4668 |
final boolean withGaps = submitGaps; |
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260 |
4668 |
JMenuItem method = new JMenuItem(MessageManager.formatMessage( |
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"label.calcname_with_default_settings", new String[] |
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{ calcName })); |
263 |
4668 |
method.setToolTipText(MessageManager.formatMessage( |
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"label.action_with_default_settings", new String[] |
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{ action })); |
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method.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
269 |
0 |
@Override... |
270 |
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public void actionPerformed(ActionEvent e) |
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{ |
272 |
0 |
AlignmentView msa = alignFrame.gatherSequencesForAlignment(); |
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274 |
0 |
if (msa != null) |
275 |
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{ |
276 |
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new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps, |
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true, |
278 |
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alignFrame.getViewport().getAlignment().getDataset(), |
279 |
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alignFrame); |
280 |
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} |
281 |
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|
282 |
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} |
283 |
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}); |
284 |
4668 |
msawsmenu.add(method); |
285 |
4668 |
if (hasparams) |
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{ |
287 |
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|
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|
289 |
4668 |
method = new JMenuItem( |
290 |
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MessageManager.getString("label.edit_settings_and_run")); |
291 |
4668 |
method.setToolTipText(MessageManager.getString( |
292 |
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"label.view_and_change_parameters_before_alignment")); |
293 |
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|
294 |
4668 |
method.addActionListener(new ActionListener() |
295 |
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{ |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
296 |
0 |
@Override... |
297 |
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public void actionPerformed(ActionEvent e) |
298 |
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{ |
299 |
0 |
AlignmentView msa = alignFrame.gatherSequencesForAlignment(); |
300 |
0 |
if (msa != null) |
301 |
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{ |
302 |
0 |
new MsaWSClient(service, null, null, true, |
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alignFrame.getTitle(), msa, withGaps, true, |
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alignFrame.getViewport().getAlignment().getDataset(), |
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alignFrame); |
306 |
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} |
307 |
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|
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} |
309 |
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}); |
310 |
4668 |
msawsmenu.add(method); |
311 |
4668 |
List<WsParamSetI> presets = service.getParamStore().getPresets(); |
312 |
4668 |
if (presets != null && presets.size() > 0) |
313 |
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{ |
314 |
2338 |
JMenu presetlist = new JMenu(MessageManager.formatMessage( |
315 |
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"label.run_with_preset_params", new String[] |
316 |
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{ calcName })); |
317 |
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|
318 |
2338 |
final int showToolTipFor = ToolTipManager.sharedInstance() |
319 |
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.getDismissDelay(); |
320 |
2338 |
for (final WsParamSetI preset : presets) |
321 |
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{ |
322 |
5600 |
final JMenuItem methodR = new JMenuItem(preset.getName()); |
323 |
5600 |
final int QUICK_TOOLTIP = 1500; |
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|
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326 |
5600 |
methodR.addMouseListener(new MouseAdapter() |
327 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
328 |
0 |
@Override... |
329 |
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public void mouseEntered(MouseEvent e) |
330 |
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{ |
331 |
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ToolTipManager.sharedInstance() |
332 |
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.setDismissDelay(QUICK_TOOLTIP); |
333 |
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} |
334 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
335 |
0 |
@Override... |
336 |
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public void mouseExited(MouseEvent e) |
337 |
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{ |
338 |
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ToolTipManager.sharedInstance() |
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.setDismissDelay(showToolTipFor); |
340 |
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} |
341 |
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}); |
343 |
5600 |
String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>" |
344 |
5600 |
+ (preset.isModifiable() |
345 |
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? MessageManager.getString("label.user_preset") |
346 |
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: MessageManager |
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.getString("label.service_preset")) |
348 |
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+ "</strong><br/>" + preset.getDescription()); |
349 |
5600 |
methodR.setToolTipText(tooltip); |
350 |
5600 |
methodR.addActionListener(new ActionListener() |
351 |
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{ |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
352 |
0 |
@Override... |
353 |
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public void actionPerformed(ActionEvent e) |
354 |
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{ |
355 |
0 |
AlignmentView msa = alignFrame |
356 |
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.gatherSequencesForAlignment(); |
357 |
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|
358 |
0 |
if (msa != null) |
359 |
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{ |
360 |
0 |
MsaWSClient msac = new MsaWSClient(service, preset, |
361 |
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alignFrame.getTitle(), msa, false, true, |
362 |
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alignFrame.getViewport().getAlignment() |
363 |
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.getDataset(), |
364 |
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alignFrame); |
365 |
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} |
366 |
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|
367 |
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} |
368 |
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|
369 |
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}); |
370 |
5600 |
presetlist.add(methodR); |
371 |
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} |
372 |
2338 |
msawsmenu.add(presetlist); |
373 |
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} |
374 |
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} |
375 |
4668 |
if (!submitGaps && canSubmitGaps()) |
376 |
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{ |
377 |
932 |
submitGaps = true; |
378 |
932 |
finished = false; |
379 |
|
} |
380 |
|
else |
381 |
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{ |
382 |
3736 |
finished = true; |
383 |
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} |
384 |
4668 |
} while (!finished); |
385 |
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} |
386 |
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} |