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src/bzh/plealog/blastviewer/actions/summary/ViewQueryIprScanPredictionsAction.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| /* Copyright (C) 2021 Patrick G. Durand | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * https://www.gnu.org/licenses/agpl-3.0.txt | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| */ | ||
| package bzh.plealog.blastviewer.actions.summary; | ||
|
|
||
| import java.awt.event.ActionEvent; | ||
|
|
||
| import javax.swing.AbstractAction; | ||
| import javax.swing.Icon; | ||
| import javax.swing.JOptionPane; | ||
| import javax.swing.SwingUtilities; | ||
|
|
||
| import com.plealog.genericapp.api.EZEnvironment; | ||
| import com.plealog.genericapp.api.log.EZLogger; | ||
|
|
||
| import bzh.plealog.bioinfo.api.data.searchresult.SROutput; | ||
| import bzh.plealog.bioinfo.ui.blast.resulttable.SummaryTable; | ||
| import bzh.plealog.bioinfo.ui.blast.resulttable.SummaryTableModel; | ||
| import bzh.plealog.blastviewer.resources.BVMessages; | ||
| import bzh.plealog.blastviewer.summary.ViewQueryIprScanPredictionsDialog; | ||
|
|
||
| /** | ||
| * This class implements the action to view Interposcan predictions | ||
| * made on a query. | ||
| * | ||
| * @author Patrick G. Durand | ||
| */ | ||
| public class ViewQueryIprScanPredictionsAction extends AbstractAction { | ||
| private static final long serialVersionUID = -3984245135396746453L; | ||
| private SummaryTable _table; | ||
| private boolean _running = false; | ||
|
|
||
| /** | ||
| * Action constructor. | ||
| * | ||
| * @param name | ||
| * the name of the action. | ||
| */ | ||
| public ViewQueryIprScanPredictionsAction(String name) { | ||
| super(name); | ||
| } | ||
|
|
||
| /** | ||
| * Action constructor. | ||
| * | ||
| * @param name | ||
| * the name of the action. | ||
| * @param icon | ||
| * the icon of the action. | ||
| */ | ||
| public ViewQueryIprScanPredictionsAction(String name, Icon icon) { | ||
| super(name, icon); | ||
| } | ||
|
|
||
| /** | ||
| * Set data object. | ||
| */ | ||
| public void setTable(SummaryTable table) { | ||
| _table = table; | ||
| } | ||
|
|
||
| private void doAction() { | ||
| if (_running || _table==null || _table.getSelectedRowCount()!=1) | ||
| return; | ||
|
|
||
| _running = true; | ||
|
|
||
| //get selected SROuput | ||
| SROutput sro = (SROutput) _table.getValueAt( | ||
| _table.getSelectedRow(), | ||
| SummaryTableModel.RESULT_DATA_COL); | ||
| if (sro.isEmpty()) { | ||
| return; | ||
| } | ||
|
|
||
| ViewQueryIprScanPredictionsDialog dlg = new ViewQueryIprScanPredictionsDialog( | ||
| JOptionPane.getFrameForComponent(_table), sro.getIteration(0).getIterationQueryID()); | ||
|
|
||
| dlg.setData(sro.getIteration(0).getIterationQueryFeatureTable(), sro.getIteration(0).getIterationQueryLength()); | ||
| dlg.setVisible(true); | ||
| } | ||
|
|
||
| public void actionPerformed(ActionEvent event) { | ||
| SwingUtilities.invokeLater(new Runnable() { | ||
| @Override | ||
| public void run() { | ||
| try { | ||
| doAction(); | ||
| } catch (Throwable t) { | ||
| EZLogger.warn(BVMessages.getString("OpenFileAction.err") | ||
| + t.toString()); | ||
| } finally { | ||
| _running = false; | ||
| EZEnvironment.setDefaultCursor(); | ||
| } | ||
| } | ||
| }); | ||
| } | ||
|
|
||
| } |
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113 changes: 113 additions & 0 deletions
113
src/bzh/plealog/blastviewer/summary/ViewQueryIprScanPredictionsDialog.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| /* Copyright (C) 2021 Patrick G. Durand | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * https://www.gnu.org/licenses/agpl-3.0.txt | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| */ | ||
| package bzh.plealog.blastviewer.summary; | ||
|
|
||
| import java.awt.BorderLayout; | ||
| import java.awt.Dimension; | ||
| import java.awt.FlowLayout; | ||
| import java.awt.Frame; | ||
| import java.awt.event.ActionEvent; | ||
| import java.awt.event.ActionListener; | ||
|
|
||
| import javax.swing.JButton; | ||
| import javax.swing.JDialog; | ||
| import javax.swing.JPanel; | ||
|
|
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| import bzh.plealog.bioinfo.api.data.feature.FeatureTable; | ||
| import bzh.plealog.bioinfo.api.data.sequence.BankSequenceDescriptor; | ||
| import bzh.plealog.bioinfo.data.sequence.EmptySequence; | ||
| import bzh.plealog.bioinfo.ui.feature.FeatureViewerFactory; | ||
| import bzh.plealog.bioinfo.ui.sequence.extended.CombinedAnnotatedSequenceViewer; | ||
| import bzh.plealog.bioinfo.util.DAlphabetUtils; | ||
| import bzh.plealog.blastviewer.resources.BVMessages; | ||
|
|
||
| /** | ||
| * Dialogue box to display Interprosan predictions. | ||
| * | ||
| * @author Patrick G. Durand | ||
| */ | ||
| public class ViewQueryIprScanPredictionsDialog extends JDialog { | ||
| private static final long serialVersionUID = 5928719684421848123L; | ||
|
|
||
| private CombinedAnnotatedSequenceViewer _viewer; | ||
| private JPanel _resultPanel; | ||
| private Dimension _startingSize = new Dimension(840,480); | ||
|
|
||
| /** | ||
| * Constructor. | ||
| * | ||
| * @param parent parent frame | ||
| * @param queryID query ID shown in dialogue header | ||
| */ | ||
| public ViewQueryIprScanPredictionsDialog(Frame parent, String queryID) { | ||
| super(parent); | ||
| setLocationByPlatform(true); | ||
| setPreferredSize(_startingSize); | ||
| setSize(_startingSize); | ||
| setTitle(String.format( | ||
| BVMessages.getString("EditQueryClassificationDialog.this.title"), queryID)); | ||
|
|
||
| _resultPanel = new JPanel(new BorderLayout()); | ||
| _viewer = new CombinedAnnotatedSequenceViewer( | ||
| null, BVMessages.class.getResourceAsStream("featureWebLink.conf"), | ||
| false, false, false, false, false, true, false, false, | ||
| FeatureViewerFactory.TYPE.COMBO); | ||
| _resultPanel.add(_viewer); | ||
| getContentPane().add(_resultPanel, BorderLayout.CENTER); | ||
|
|
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| JPanel panel = new JPanel(); | ||
| getContentPane().add(panel, BorderLayout.SOUTH); | ||
| panel.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 5)); | ||
|
|
||
| JButton btnOk = new JButton( | ||
| BVMessages.getString("EditQueryClassificationDialog.btnOk.text")); | ||
| btnOk.setPreferredSize(new Dimension(65, 23)); | ||
| btnOk.setMinimumSize(new Dimension(65, 23)); | ||
| btnOk.setMaximumSize(new Dimension(65, 23)); | ||
| btnOk.addActionListener(new OkListener()); | ||
| panel.add(btnOk); | ||
|
|
||
| this.setModal(true); | ||
| this.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); | ||
| // to center | ||
| this.setLocationRelativeTo(null); | ||
| } | ||
|
|
||
| /** | ||
| * Set data. | ||
| * | ||
| * @param ft feature table | ||
| * @param seqsize size of query sequence | ||
| */ | ||
| public void setData(FeatureTable ft, int seqsize) { | ||
| BankSequenceDescriptor sd = new BankSequenceDescriptor( | ||
| ft, null, new EmptySequence(DAlphabetUtils.getIUPAC_DNA_Alphabet(), seqsize)); | ||
| _viewer.setData(sd); | ||
| } | ||
|
|
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| private void close() { | ||
| dispose(); | ||
| } | ||
|
|
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| private class OkListener implements ActionListener { | ||
|
|
||
| @Override | ||
| public void actionPerformed(ActionEvent e) { | ||
| close(); | ||
| } | ||
| } | ||
| } |
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