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Merge pull request #18 from sc13-bioinf/master
Move the specification of the MT chromosome to Select Reference dialog
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <form xmlns="http://www.intellij.com/uidesigner/form/" version="1" bind-to-class="IO.ReferenceDialog"> | ||
| <grid id="cbd77" binding="contentPane" layout-manager="GridLayoutManager" row-count="2" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1"> | ||
| <margin top="10" left="10" bottom="10" right="10"/> | ||
| <constraints> | ||
| <xy x="48" y="54" width="436" height="297"/> | ||
| </constraints> | ||
| <properties/> | ||
| <border type="none"/> | ||
| <children> | ||
| <grid id="94766" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1"> | ||
| <margin top="0" left="0" bottom="0" right="0"/> | ||
| <constraints> | ||
| <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="1" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| <properties/> | ||
| <border type="none"/> | ||
| <children> | ||
| <hspacer id="98af6"> | ||
| <constraints> | ||
| <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="1" hsize-policy="6" anchor="0" fill="1" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| </hspacer> | ||
| <grid id="9538f" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="true" same-size-vertically="false" hgap="-1" vgap="-1"> | ||
| <margin top="0" left="0" bottom="0" right="0"/> | ||
| <constraints> | ||
| <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| <properties/> | ||
| <border type="none"/> | ||
| <children> | ||
| <component id="e7465" class="javax.swing.JButton" binding="buttonOK"> | ||
| <constraints> | ||
| <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| <properties> | ||
| <text value="OK"/> | ||
| </properties> | ||
| </component> | ||
| <component id="5723f" class="javax.swing.JButton" binding="buttonCancel"> | ||
| <constraints> | ||
| <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| <properties> | ||
| <text value="Cancel"/> | ||
| </properties> | ||
| </component> | ||
| </children> | ||
| </grid> | ||
| </children> | ||
| </grid> | ||
| <grid id="e3588" layout-manager="GridLayoutManager" row-count="3" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1"> | ||
| <margin top="0" left="0" bottom="0" right="0"/> | ||
| <constraints> | ||
| <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| <properties/> | ||
| <border type="none"/> | ||
| <children> | ||
| <component id="49622" class="javax.swing.JButton" binding="referenceButton" default-binding="true"> | ||
| <constraints> | ||
| <grid row="0" column="0" row-span="1" col-span="2" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| <properties> | ||
| <text value="Select Reference"/> | ||
| <toolTipText value="Select your reference sequence in FASTA format here. You do not need to create indices, these will be created if required by the pipeline itself."/> | ||
| </properties> | ||
| </component> | ||
| <component id="cfc90" class="javax.swing.JLabel"> | ||
| <constraints> | ||
| <grid row="2" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/> | ||
| </constraints> | ||
| <properties> | ||
| <text value="Name of mitochondrial chromosome"/> | ||
| </properties> | ||
| </component> | ||
| <component id="18bd9" class="javax.swing.JTextField" binding="mtcapture_jtextfield"> | ||
| <constraints> | ||
| <grid row="2" column="1" row-span="1" col-span="1" vsize-policy="0" hsize-policy="6" anchor="8" fill="1" indent="0" use-parent-layout="false"> | ||
| <preferred-size width="150" height="-1"/> | ||
| </grid> | ||
| </constraints> | ||
| <properties> | ||
| <toolTipText value="Enter the ID of the MT chromosome here."/> | ||
| </properties> | ||
| </component> | ||
| <component id="a9522" class="javax.swing.JTextPane" binding="pleaseInputTheNameTextPane" default-binding="true"> | ||
| <constraints> | ||
| <grid row="1" column="0" row-span="1" col-span="2" vsize-policy="7" hsize-policy="6" anchor="0" fill="3" indent="0" use-parent-layout="false"> | ||
| <preferred-size width="150" height="40"/> | ||
| </grid> | ||
| </constraints> | ||
| <properties> | ||
| <text value="Please input the name of the mitochondrial chromosome. This is used in calculating coverage statistics and for MT capture experiments. Remember to use chrMT for HG19 and MT for hs37d5"/> | ||
| </properties> | ||
| </component> | ||
| </children> | ||
| </grid> | ||
| </children> | ||
| </grid> | ||
| </form> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| package IO; | ||
|
|
||
| import javax.swing.*; | ||
| import java.awt.*; | ||
| import java.awt.event.*; | ||
|
|
||
| public class ReferenceDialog extends JDialog { | ||
| private JPanel contentPane; | ||
| private JButton buttonOK; | ||
| private JButton buttonCancel; | ||
| private JButton referenceButton; | ||
| private JTextField mtcapture_jtextfield; | ||
| private JTextPane pleaseInputTheNameTextPane; | ||
| private Communicator communicator; | ||
| private JButton runButton; | ||
|
|
||
| public ReferenceDialog(final Communicator communicator, JButton runButton) { | ||
| setContentPane(contentPane); | ||
| setModal(true); | ||
| getRootPane().setDefaultButton(buttonOK); | ||
| mtcapture_jtextfield.setText(communicator.getFilter_for_mt()); | ||
| this.communicator = communicator; | ||
| this.runButton = runButton; | ||
|
|
||
| buttonOK.addActionListener(new ActionListener() { | ||
| public void actionPerformed(ActionEvent e) { | ||
| onOK(); | ||
| } | ||
| }); | ||
|
|
||
| buttonCancel.addActionListener(new ActionListener() { | ||
| public void actionPerformed(ActionEvent e) { | ||
| onCancel(); | ||
| } | ||
| }); | ||
|
|
||
| referenceButton.addActionListener(new ActionListener() { | ||
| @Override | ||
| public void actionPerformed(ActionEvent actionEvent) { | ||
| ReferenceFastAChooser rffqc = new ReferenceFastAChooser(communicator); | ||
| referenceButton.setForeground(Color.green); | ||
|
|
||
| if (checkIfInputWasSelected()) { | ||
| runButton.setEnabled(true); | ||
| buttonOK.setEnabled(true); | ||
| } else { | ||
| runButton.setEnabled(false); | ||
| buttonCancel.setEnabled(false); | ||
| } | ||
| } | ||
| }); | ||
|
|
||
| // call onCancel() when cross is clicked | ||
| setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); | ||
| addWindowListener(new WindowAdapter() { | ||
| public void windowClosing(WindowEvent e) { | ||
| onCancel(); | ||
| } | ||
| }); | ||
|
|
||
| // call onCancel() on ESCAPE | ||
| contentPane.registerKeyboardAction(new ActionListener() { | ||
| public void actionPerformed(ActionEvent e) { | ||
| onCancel(); | ||
| } | ||
| }, KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); | ||
| } | ||
|
|
||
| private void onOK() { | ||
| // add your code here | ||
| this.communicator.setFilter_for_mt(this.mtcapture_jtextfield.getText()); | ||
| dispose(); | ||
| } | ||
|
|
||
| private void onCancel() { | ||
| // add your code here if necessary | ||
| dispose(); | ||
| } | ||
|
|
||
| private boolean checkIfInputWasSelected() { | ||
| boolean tmp = false; | ||
| if (communicator.getGUI_inputfiles() != null && communicator.getGUI_reference() != null && communicator.getGUI_resultspath() != null) { | ||
| if(communicator.getGUI_inputfiles().size() != 0){ | ||
| tmp = true; | ||
| } | ||
| } | ||
| return tmp; | ||
| } | ||
| } |
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