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Added a dialog for approving loss of function @27
Added a popup for making an annotatin without drag and drop @29 Fixed refresh of tree after expand/collapse of nodes @28
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| v2.22 | ||
| v2.23 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,144 @@ | ||
| /* | ||
| * | ||
| * Copyright (c) 2010, Regents of the University of California | ||
| * All rights reserved. | ||
| * | ||
| * Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: | ||
| * | ||
| * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. | ||
| * Neither the name of the Lawrence Berkeley National Lab nor the names of its contributors may be used to endorse | ||
| * or promote products derived from this software without specific prior written permission. | ||
| * | ||
| * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, | ||
| * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. | ||
| * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, | ||
| * OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; | ||
| * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | ||
| * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| * | ||
| */ | ||
|
|
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| package org.paint.dialog; | ||
|
|
||
| import java.awt.BorderLayout; | ||
| import java.awt.Color; | ||
| import java.awt.Dimension; | ||
| import java.awt.Frame; | ||
| import java.awt.event.ActionEvent; | ||
| import java.awt.event.ActionListener; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
|
|
||
| import javax.swing.BorderFactory; | ||
| import javax.swing.Box; | ||
| import javax.swing.BoxLayout; | ||
| import javax.swing.JButton; | ||
| import javax.swing.JCheckBox; | ||
| import javax.swing.JDialog; | ||
| import javax.swing.JLabel; | ||
| import javax.swing.JPanel; | ||
| import javax.swing.border.Border; | ||
|
|
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| import org.bbop.phylo.util.OWLutil; | ||
| import org.paint.util.RenderUtil; | ||
|
|
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| import owltools.gaf.species.TaxonFinder; | ||
|
|
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| public class TaxonDialog extends JDialog { | ||
| /** | ||
| * | ||
| */ | ||
| private static final long serialVersionUID = 1L; | ||
|
|
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| Map<JCheckBox, Integer> selections; | ||
| boolean loss; | ||
|
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| /** Creates the GUI shown inside the frame's content pane. */ | ||
| public TaxonDialog(Frame frame, String go_id, List<String> invalids) { | ||
| super(frame, true); | ||
| setLayout(new BorderLayout()); | ||
| setContentPane(taxonPane(go_id, invalids)); | ||
| pack(); | ||
| setLocationRelativeTo(frame); | ||
| setVisible(true); | ||
| } | ||
|
|
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| public boolean isLost() { | ||
| // this.paintComponents(this.getGraphics()); | ||
| return loss; | ||
| } | ||
|
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| private JPanel taxonPane (String go_id, List<String> invalids) { | ||
| JPanel qualify = new JPanel(); | ||
| qualify.setLayout(new BoxLayout(qualify, BoxLayout.PAGE_AXIS)); | ||
|
|
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| //Create the components. | ||
| JPanel selectionPane = createTaxaListPane(go_id, invalids); | ||
|
|
||
| //Lay them out. | ||
|
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| JPanel buttonPane = new JPanel(); | ||
| buttonPane.setOpaque(true); | ||
| buttonPane.setBackground(RenderUtil.getAspectColor()); | ||
| JButton lossButton = null; | ||
| lossButton = new JButton("Set as loss"); | ||
| lossButton.addActionListener(new ActionListener() { | ||
| public void actionPerformed(ActionEvent e) { | ||
| loss = true; | ||
| TaxonDialog.this.dispose(); | ||
| } | ||
| } ); | ||
| JButton cancelButton = null; | ||
| cancelButton = new JButton("Cancel"); | ||
| getRootPane().setDefaultButton(cancelButton); | ||
| cancelButton.addActionListener(new ActionListener() { | ||
| public void actionPerformed(ActionEvent e) { | ||
| loss = false; | ||
| TaxonDialog.this.dispose(); | ||
| } | ||
| } ); | ||
|
|
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| buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.LINE_AXIS)); | ||
| buttonPane.setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10)); | ||
| buttonPane.add(Box.createHorizontalGlue()); | ||
| buttonPane.add(Box.createRigidArea(new Dimension(10, 0))); | ||
| buttonPane.add(lossButton); | ||
| buttonPane.add(Box.createRigidArea(new Dimension(10, 0))); | ||
| buttonPane.add(cancelButton); | ||
| buttonPane.add(Box.createRigidArea(new Dimension(10, 0))); | ||
|
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| qualify.add(selectionPane); | ||
| qualify.add(buttonPane); | ||
| return qualify; | ||
| } | ||
|
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| /** Creates the panel shown by the first tab. */ | ||
| private JPanel createTaxaListPane(String go_id, List<String> invalids) { | ||
| String description; | ||
| description = "Do you intend the evolutionary loss of " + OWLutil.inst().getTermLabel(go_id) + " in these taxa?"; | ||
|
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| JPanel box = new JPanel(); | ||
| JLabel label = new JLabel(description); | ||
| label.setBorder(BorderFactory.createEmptyBorder(10,10,10,10)); | ||
| box.setOpaque(true); | ||
| box.setBackground(RenderUtil.getAspectColor()); | ||
|
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| box.setLayout(new BoxLayout(box, BoxLayout.PAGE_AXIS)); | ||
| box.add(label); | ||
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| for (String taxon : invalids) { | ||
| label = new JLabel(TaxonFinder.getSpecies(taxon)); | ||
| label.setBackground(Color.white); | ||
| label.setOpaque(true); | ||
| box.add(label); | ||
| } | ||
| JPanel pane = new JPanel(new BorderLayout()); | ||
| pane.add(box, BorderLayout.PAGE_START); | ||
| Border padding = BorderFactory.createEmptyBorder(20,20,5,20); | ||
| pane.setBorder(padding); | ||
| pane.setOpaque(true); | ||
| pane.setBackground(RenderUtil.getAspectColor()); | ||
| return pane; | ||
| } | ||
|
|
||
| } |
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