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Revision a862b815

IDa862b815b9f46f7d240201146bfa6dfa77a7f35a
Parent 00d1a6ce
Child ecd0d355

Added by Ben Stöver about 4 years ago

Missing files from last commit added.

View differences:

eu.etaxonomy.taxeditor.cdmlib/.classpath
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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	<classpathentry exported="true" kind="lib" path="lib/c3p0-0.9.5.2.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-4.4.0-SNAPSHOT.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-4.4.0-SNAPSHOT.jar" sourcepath="C:/Users/k.luther/.m2/repository/eu/etaxonomy/cdmlib-ext/4.3.0-SNAPSHOT/cdmlib-ext-4.4.0-SNAPSHOT-sources.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-io-4.4.0-SNAPSHOT.jar" sourcepath="C:/Users/k.luther/.m2/repository/eu/etaxonomy/cdmlib-io/4.3.0-SNAPSHOT/cdmlib-io-4.4.0-SNAPSHOT-sources.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-model-4.4.0-SNAPSHOT.jar" sourcepath="C:/Users/k.luther/.m2/repository/eu/etaxonomy/cdmlib-model/4.3.0-SNAPSHOT/cdmlib-model-4.4.0-SNAPSHOT-sources.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-4.4.0-SNAPSHOT.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-print-4.4.0-SNAPSHOT.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-4.4.0-SNAPSHOT.jar"/>
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	<classpathentry exported="true" kind="lib" path="lib/cdmlib-services-4.4.0-SNAPSHOT.jar" sourcepath="C:/Users/k.luther/.m2/repository/eu/etaxonomy/cdmlib-services/4.3.0-SNAPSHOT/cdmlib-services-4.4.0-SNAPSHOT-sources.jar"/>
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185
	<classpathentry exported="true" kind="lib" path="lib/solr-core-3.6.2.jar"/>
186
	<classpathentry exported="true" kind="lib" path="lib/solr-solrj-3.6.2.jar"/>
187
	<classpathentry exported="true" kind="lib" path="lib/spring-aop-4.2.4.RELEASE.jar"/>
188
	<classpathentry exported="true" kind="lib" path="lib/spring-aspects-4.2.4.RELEASE.jar"/>
189
	<classpathentry exported="true" kind="lib" path="lib/spring-beans-4.2.4.RELEASE.jar"/>
190
	<classpathentry exported="true" kind="lib" path="lib/spring-context-4.2.4.RELEASE.jar"/>
191
	<classpathentry exported="true" kind="lib" path="lib/spring-context-support-4.2.4.RELEASE.jar"/>
192
	<classpathentry exported="true" kind="lib" path="lib/spring-core-4.2.4.RELEASE.jar"/>
193
	<classpathentry exported="true" kind="lib" path="lib/spring-expression-4.2.4.RELEASE.jar"/>
194
	<classpathentry exported="true" kind="lib" path="lib/spring-jdbc-4.2.4.RELEASE.jar"/>
195
	<classpathentry exported="true" kind="lib" path="lib/spring-modules-cache-0.7.jar"/>
196
	<classpathentry exported="true" kind="lib" path="lib/spring-orm-4.2.4.RELEASE.jar"/>
197
	<classpathentry exported="true" kind="lib" path="lib/spring-oxm-4.2.4.RELEASE.jar"/>
198
	<classpathentry exported="true" kind="lib" path="lib/spring-plugin-core-1.2.0.RELEASE.jar"/>
199
	<classpathentry exported="true" kind="lib" path="lib/spring-plugin-metadata-1.2.0.RELEASE.jar"/>
200
	<classpathentry exported="true" kind="lib" path="lib/spring-security-config-4.0.3.RELEASE.jar"/>
201
	<classpathentry exported="true" kind="lib" path="lib/spring-security-core-4.0.3.RELEASE.jar"/>
202
	<classpathentry exported="true" kind="lib" path="lib/spring-security-web-4.0.3.RELEASE.jar"/>
203
	<classpathentry exported="true" kind="lib" path="lib/spring-test-4.2.4.RELEASE.jar"/>
204
	<classpathentry exported="true" kind="lib" path="lib/spring-tx-4.2.4.RELEASE.jar"/>
205
	<classpathentry exported="true" kind="lib" path="lib/spring-web-4.2.4.RELEASE.jar"/>
206
	<classpathentry exported="true" kind="lib" path="lib/spring-webmvc-4.2.4.RELEASE.jar"/>
207
	<classpathentry exported="true" kind="lib" path="lib/springfox-core-2.3.1.jar"/>
208
	<classpathentry exported="true" kind="lib" path="lib/springfox-schema-2.3.1.jar"/>
209
	<classpathentry exported="true" kind="lib" path="lib/springfox-spi-2.3.1.jar"/>
210
	<classpathentry exported="true" kind="lib" path="lib/springfox-spring-web-2.3.1.jar"/>
211
	<classpathentry exported="true" kind="lib" path="lib/springfox-swagger-common-2.3.1.jar"/>
212
	<classpathentry exported="true" kind="lib" path="lib/springfox-swagger2-2.3.1.jar"/>
213
	<classpathentry exported="true" kind="lib" path="lib/standard-1.1.2.jar"/>
214
	<classpathentry exported="true" kind="lib" path="lib/stax-1.2.0.jar"/>
215
	<classpathentry exported="true" kind="lib" path="lib/stax-api-1.0.1.jar"/>
216
	<classpathentry exported="true" kind="lib" path="lib/stax-ex-1.7.7.jar"/>
217
	<classpathentry exported="true" kind="lib" path="lib/swagger-annotations-1.5.6.jar"/>
218
	<classpathentry exported="true" kind="lib" path="lib/swagger-models-1.5.5.jar"/>
219
	<classpathentry exported="true" kind="lib" path="lib/tools.jar"/>
220
	<classpathentry exported="true" kind="lib" path="lib/txw2-2.2.11.jar"/>
221
	<classpathentry exported="true" kind="lib" path="lib/unitils-core-3.4.2.jar"/>
222
	<classpathentry exported="true" kind="lib" path="lib/unitils-database-3.4.2.jar"/>
223
	<classpathentry exported="true" kind="lib" path="lib/unitils-dbmaintainer-3.4.2.jar"/>
224
	<classpathentry exported="true" kind="lib" path="lib/unitils-dbunit-3.4.2.jar"/>
225
	<classpathentry exported="true" kind="lib" path="lib/unitils-easymock-3.4.2.jar"/>
226
	<classpathentry exported="true" kind="lib" path="lib/unitils-inject-3.4.2.jar"/>
227
	<classpathentry exported="true" kind="lib" path="lib/unitils-mock-3.4.2.jar"/>
228
	<classpathentry exported="true" kind="lib" path="lib/unitils-orm-3.4.2.jar"/>
229
	<classpathentry exported="true" kind="lib" path="lib/unitils-spring-3.4.2.jar"/>
230
	<classpathentry exported="true" kind="lib" path="lib/usertype.jodatime-2.0.1.jar"/>
231
	<classpathentry exported="true" kind="lib" path="lib/usertype.spi-2.0.1.jar"/>
232
	<classpathentry exported="true" kind="lib" path="lib/validation-api-1.1.0.Final.jar"/>
233
	<classpathentry exported="true" kind="lib" path="lib/wsdl4j-1.6.3.jar"/>
234
	<classpathentry exported="true" kind="lib" path="lib/xalan-2.7.0.jar"/>
235
	<classpathentry exported="true" kind="lib" path="lib/xercesImpl-2.11.0.jar"/>
236
	<classpathentry exported="true" kind="lib" path="lib/xml-apis-1.0.b2.jar"/>
237
	<classpathentry exported="true" kind="lib" path="lib/xml-apis-ext-1.3.04.jar"/>
238
	<classpathentry exported="true" kind="lib" path="lib/xml-resolver-1.2.jar"/>
239
	<classpathentry exported="true" kind="lib" path="lib/xmlbeans-2.6.0.jar"/>
240
	<classpathentry exported="true" kind="lib" path="lib/xmlgraphics-commons-1.5.jar"/>
241
	<classpathentry exported="true" kind="lib" path="lib/xmlpull-1.1.3.1.jar"/>
242
	<classpathentry exported="true" kind="lib" path="lib/xmlunit-1.6.jar"/>
243
	<classpathentry exported="true" kind="lib" path="lib/xom-1.2.5.jar"/>
244
	<classpathentry exported="true" kind="lib" path="lib/xpp3_min-1.1.4c.jar"/>
245
	<classpathentry exported="true" kind="lib" path="lib/xpp3-1.1.4c.jar"/>
246
	<classpathentry exported="true" kind="lib" path="lib/xsom-20140925.jar"/>
247
	<classpathentry exported="true" kind="lib" path="lib/xstream-1.4.8.jar"/>
248
	<classpathentry exported="true" kind="lib" path="lib/yjp-controller-api-redist-9.0.8.jar"/>
249
	<classpathentry exported="true" kind="lib" path="lib/spring-security-oauth2-2.0.11.RELEASE.jar"/>
250
	<classpathentry kind="output" path="target/classes"/>
251
</classpath>
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/AbstractExportSingleReadAlignmentWizardPage.java
1
/**
2
* Copyright (C) 2016 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9
package eu.etaxonomy.taxeditor.molecular.io.wizard;
10

  
11

  
12
import org.eclipse.jface.resource.ImageDescriptor;
13
import org.eclipse.jface.wizard.WizardPage;
14

  
15

  
16

  
17
/**
18
 * @author bstoe_01
19
 * @date 18.11.2016
20
 *
21
 */
22
public abstract class AbstractExportSingleReadAlignmentWizardPage extends WizardPage {
23
    public AbstractExportSingleReadAlignmentWizardPage(String pageName, String title, ImageDescriptor titleImage) {
24
        super(pageName, title, titleImage);
25
    }
26

  
27

  
28
    public AbstractExportSingleReadAlignmentWizardPage(String pageName) {
29
        super(pageName);
30
    }
31

  
32

  
33
    /**
34
     * {@inheritDoc}
35
     */
36
    @Override
37
    public ExportSingleReadAlignmentWizard getWizard() {
38
        return (ExportSingleReadAlignmentWizard)super.getWizard();  // Would throw an exception, if this page is used within another wizard.
39
    }
40
}
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentOptionsPage.java
1
// $Id$
2
/**
3
* Copyright (C) 2016 EDIT
4
* European Distributed Institute of Taxonomy
5
* http://www.e-taxonomy.eu
6
*
7
* The contents of this file are subject to the Mozilla Public License Version 1.1
8
* See LICENSE.TXT at the top of this package for the full license terms.
9
*/
10
package eu.etaxonomy.taxeditor.molecular.io.wizard;
11

  
12

  
13
import org.eclipse.core.databinding.DataBindingContext;
14
import org.eclipse.core.databinding.validation.MultiValidator;
15
import org.eclipse.core.databinding.validation.ValidationStatus;
16
import org.eclipse.core.runtime.IStatus;
17
import org.eclipse.jface.databinding.swt.ISWTObservableValue;
18
import org.eclipse.jface.databinding.swt.SWTObservables;
19
import org.eclipse.jface.databinding.wizard.WizardPageSupport;
20
import org.eclipse.swt.SWT;
21
import org.eclipse.swt.events.SelectionAdapter;
22
import org.eclipse.swt.events.SelectionEvent;
23
import org.eclipse.swt.layout.FormAttachment;
24
import org.eclipse.swt.layout.FormData;
25
import org.eclipse.swt.layout.FormLayout;
26
import org.eclipse.swt.widgets.Button;
27
import org.eclipse.swt.widgets.Composite;
28
import org.eclipse.swt.widgets.Label;
29
import org.eclipse.swt.widgets.Text;
30

  
31
import eu.etaxonomy.taxeditor.molecular.Messages;
32

  
33

  
34

  
35
/**
36
 * Wizard page that allows to specify which parts of a single read alignment shall be exported to an alignment file.
37
 *
38
 * @author Ben St&ouml;ver
39
 * @date 18.04.2016
40
 */
41
public class ExportSingleReadAlignmentOptionsPage extends AbstractExportSingleReadAlignmentWizardPage {
42
    private Text consensusSequenceLabelTextField;
43
    private Button exportConsensusSequenceCB;
44
    private Button exportSingleReadsCB;
45
    private Button gapRadioButton;
46
    private Button missingDataRadioButton;
47
    private Button elongateSequecesCheckBox;
48

  
49

  
50
    /**
51
     * Create the wizard.
52
     */
53
    public ExportSingleReadAlignmentOptionsPage() {
54
        super("ExportSingleReadAlignmentOptions");  //TODO Which pageName should be used here? Any conventions? //$NON-NLS-1$
55
        setTitle("Export options");
56
        setDescription("Specify additional export parameters.");
57
    }
58

  
59

  
60
    /**
61
     * Create contents of the wizard.
62
     *
63
     * @param parent the parent component
64
     */
65
    @Override
66
    public void createControl(Composite parent) {
67
        DataBindingContext dbc = new DataBindingContext();
68
        WizardPageSupport.create(this, dbc);
69

  
70
        Composite container = new Composite(parent, SWT.NULL);
71

  
72
        setControl(container);
73
        container.setLayout(new FormLayout());
74

  
75
        exportSingleReadsCB = new Button(container, SWT.CHECK);
76
        FormData fd_exportSingleReadsCB = new FormData();
77
        fd_exportSingleReadsCB.top = new FormAttachment(0, 40);
78
        fd_exportSingleReadsCB.left = new FormAttachment(0, 10);
79
        exportSingleReadsCB.setLayoutData(fd_exportSingleReadsCB);
80
        exportSingleReadsCB.setText(Messages.wizardExportAlignmentExportSingleReads);
81
        final ISWTObservableValue exportSingleReadsObservable = SWTObservables.observeSelection(exportSingleReadsCB);
82
        dbc.bindValue(exportSingleReadsObservable, getWizard().getModel().getExportSingleReadsObservable());
83
        exportSingleReadsCB.setSelection(false);
84
        exportSingleReadsCB.setSelection(true);  // Must happen after the component has been bound to the model.
85

  
86

  
87
        exportConsensusSequenceCB = new Button(container, SWT.CHECK);
88
        exportConsensusSequenceCB.addSelectionListener(new SelectionAdapter() {
89
            @Override
90
            public void widgetSelected(SelectionEvent e) {
91
                consensusSequenceLabelTextField.setEnabled(exportConsensusSequenceCB.getSelection());
92
            }
93
        });
94
        FormData fd_exportConsensusSequenceCB = new FormData();
95
        fd_exportConsensusSequenceCB.top = new FormAttachment(exportSingleReadsCB, 6);
96
        fd_exportConsensusSequenceCB.left = new FormAttachment(0, 10);
97
        exportConsensusSequenceCB.setLayoutData(fd_exportConsensusSequenceCB);
98
        exportConsensusSequenceCB.setText(Messages.wizardExportAlignmentExportConsensusSeqLabel);
99
        final ISWTObservableValue exportConsensusSequenceObservable = SWTObservables.observeSelection(exportConsensusSequenceCB);
100
        dbc.bindValue(exportConsensusSequenceObservable, getWizard().getModel().getExportConsensusSequenceObservable());
101
        exportConsensusSequenceCB.setSelection(false);
102
        exportConsensusSequenceCB.setSelection(true);  // Must happen after the component has been bound to the model.
103

  
104
        consensusSequenceLabelTextField = new Text(container, SWT.BORDER);
105
        FormData fd_consensusSequenceNameTextField = new FormData();
106
        fd_consensusSequenceNameTextField.bottom = new FormAttachment(exportConsensusSequenceCB, 32, SWT.BOTTOM);
107
        fd_consensusSequenceNameTextField.top = new FormAttachment(exportConsensusSequenceCB, 6);
108
        fd_consensusSequenceNameTextField.right = new FormAttachment(100, -10);
109
        fd_consensusSequenceNameTextField.left = new FormAttachment(0, 32);
110
        consensusSequenceLabelTextField.setLayoutData(fd_consensusSequenceNameTextField);
111
        final ISWTObservableValue consensusSequenceLabelObservable = SWTObservables.observeText(consensusSequenceLabelTextField, SWT.Modify);
112
        dbc.bindValue(consensusSequenceLabelObservable, getWizard().getModel().getConsensusSequenceLabelObservable());
113
        consensusSequenceLabelTextField.setText("Consensus");
114

  
115
        Label lblSpecifyTheSequences = new Label(container, SWT.NONE);
116
        FormData fd_lblSpecifyTheSequences = new FormData();
117
        fd_lblSpecifyTheSequences.top = new FormAttachment(0, 10);
118
        fd_lblSpecifyTheSequences.left = new FormAttachment(0, 10);
119
        lblSpecifyTheSequences.setLayoutData(fd_lblSpecifyTheSequences);
120
        lblSpecifyTheSequences.setText("Specify the sequences to be exported:");
121

  
122
        Label lblSpecifyAdditionalExport = new Label(container, SWT.NONE);
123
        FormData fd_lblSpecifyAdditionalExport = new FormData();
124
        fd_lblSpecifyAdditionalExport.top = new FormAttachment(consensusSequenceLabelTextField, 24);
125
        fd_lblSpecifyAdditionalExport.left = new FormAttachment(exportSingleReadsCB, 0, SWT.LEFT);
126
        lblSpecifyAdditionalExport.setLayoutData(fd_lblSpecifyAdditionalExport);
127
        lblSpecifyAdditionalExport.setText("Specify additional export options:");
128

  
129
        elongateSequecesCheckBox = new Button(container, SWT.CHECK);
130
        elongateSequecesCheckBox.addSelectionListener(new SelectionAdapter() {
131
            @Override
132
            public void widgetSelected(SelectionEvent e) {
133
                missingDataRadioButton.setEnabled(elongateSequecesCheckBox.getSelection());
134
                gapRadioButton.setEnabled(elongateSequecesCheckBox.getSelection());
135
            }
136
        });
137
        FormData fd_btnElongateSequecesTo = new FormData();
138
        fd_btnElongateSequecesTo.left = new FormAttachment(exportSingleReadsCB, 0, SWT.LEFT);
139
        fd_btnElongateSequecesTo.top = new FormAttachment(lblSpecifyAdditionalExport, 12);
140
        elongateSequecesCheckBox.setLayoutData(fd_btnElongateSequecesTo);
141
        elongateSequecesCheckBox.setText("Elongate sequences to have equal length with:");
142
        dbc.bindValue(SWTObservables.observeSelection(elongateSequecesCheckBox), getWizard().getModel().getElongateSequencesObservable());
143

  
144
        missingDataRadioButton = new Button(container, SWT.RADIO);
145
        FormData fd_missingDataRadioButton = new FormData();
146
        fd_missingDataRadioButton.top = new FormAttachment(elongateSequecesCheckBox, 6);
147
        missingDataRadioButton.setLayoutData(fd_missingDataRadioButton);
148
        missingDataRadioButton.setEnabled(false);
149
        missingDataRadioButton.setText("Missing data ('?')");
150

  
151
        gapRadioButton = new Button(container, SWT.RADIO);
152
        fd_missingDataRadioButton.left = new FormAttachment(gapRadioButton, 80);
153
        FormData fd_gapRadioButton = new FormData();
154
        fd_gapRadioButton.top = new FormAttachment(elongateSequecesCheckBox, 6);
155
        fd_gapRadioButton.left = new FormAttachment(consensusSequenceLabelTextField, 0, SWT.LEFT);
156
        gapRadioButton.setLayoutData(fd_gapRadioButton);
157
        gapRadioButton.setEnabled(false);
158
        gapRadioButton.setSelection(true);
159
        gapRadioButton.setText("Gap ('-')");
160
        dbc.bindValue(SWTObservables.observeSelection(gapRadioButton), getWizard().getModel().getUseGapTokenObservable());
161

  
162
        setPageComplete(true);  // Allow to finish the wizard in the previous page.
163

  
164
        dbc.addValidationStatusProvider(new MultiValidator() {
165
            @Override
166
            protected IStatus validate() {
167
                String label = (String)consensusSequenceLabelObservable.getValue();
168
                boolean exportConsensus = (Boolean)exportConsensusSequenceObservable.getValue();
169
                boolean exportReads = (Boolean)exportSingleReadsObservable.getValue();
170

  
171
                if (!exportConsensus && !exportReads) {
172
                    return ValidationStatus.error(Messages.wizardExportAlignmentErrorNothingToExport);
173
                }
174
                else if (exportConsensus && ((label == null) || label.isEmpty())) {
175
                    return ValidationStatus.error(Messages.wizardExportAlignmentErrorMissingSeqLabel);
176
                }
177
                else {
178
                    return ValidationStatus.ok();
179
                }
180
            }
181
        });
182
    }
183
}

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