JAL-1780 Export settings for flatfile output

diff --git a/src/jalview/api/AlignExportSettingI.java b/src/jalview/api/AlignExportSettingI.java
new file mode 100644 (file)
index 0000000..cf56bf3
--- /dev/null
+++ b/src/jalview/api/AlignExportSettingI.java
@@ -0,0 +1,77 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.api;
+
+/**
+ * Abstract interface implemented by Alignment Export dialog to retrieve user
+ * configurations
+ * 
+ * @author tcnofoegbu
+ *
+ */
+public interface AlignExportSettingI
+{
+  /**
+   * Checks if hidden sequences should be exported
+   * 
+   * @return
+   */
+  public boolean isExportHiddenSequences();
+
+  /**
+   * Checks if hidden columns shoulb be exported
+   * 
+   * @return
+   */
+  public boolean isExportHiddenColumns();
+
+  /**
+   * Checks if Annotations should be exported, note this is available for
+   * complex flat file exports like JSON, HTML, GFF
+   * 
+   * @return
+   */
+  public boolean isExportAnnotations();
+
+  /**
+   * Checks if SequenceFeatures should be exported, note this is available for
+   * complex flat file exports like JSON, HTML, GFF
+   * 
+   * @return
+   */
+  public boolean isExportFeatures();
+
+  /**
+   * Checks if SequenceGroups should be exported, note this is available for
+   * complex flat file exports like JSON, HTML, GFF
+   * 
+   * @return
+   */
+  public boolean isExportGroups();
+
+  /**
+   * Checks if settings/export process is cancelled
+   * 
+   * @return
+   */
+  public boolean isCancelled();
+}

diff --git a/src/jalview/gui/AlignExportSettings.java b/src/jalview/gui/AlignExportSettings.java
new file mode 100644 (file)
index 0000000..fe7c940
--- /dev/null
+++ b/src/jalview/gui/AlignExportSettings.java
@@ -0,0 +1,115 @@
+package jalview.gui;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JDialog;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
+import jalview.api.AlignExportSettingI;
+import jalview.jbgui.GAlignExportSettings;
+
+@SuppressWarnings("serial")
+public class AlignExportSettings extends GAlignExportSettings implements
+        AlignExportSettingI
+{
+  protected JInternalFrame frame;
+
+  boolean cancelled = false;
+
+  private int width = 450;
+
+  private int height = 200;
+
+  JDialog dialog;
+
+  public AlignExportSettings(boolean hasHiddenSeq, boolean hasHiddenCols,
+          String alignFileFormat)
+  {
+    super(hasHiddenSeq, hasHiddenCols, alignFileFormat);
+
+    // frame = new JInternalFrame();
+    // frame.setContentPane(this);
+    // frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    // Desktop.addInternalFrame(frame, "Export Settings", width, height);
+
+    JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
+            JOptionPane.DEFAULT_OPTION, null, new Object[]
+            { this });
+    dialog = pane.createDialog(Desktop.desktop, "Export Settings");
+
+    // dialog = new JDialog(Desktop.instance, true);
+    // dialog.setTitle("Export Settings");
+
+    dialog.pack();
+    dialog.setVisible(true);
+
+    dialog.setContentPane(this);
+    dialog.validate();
+
+  }
+
+  // public static void main(String[] args)
+  // {
+  // new AlignExportSettings(false, false, false);
+  // }
+
+  // public void cancel_actionPerformed(ActionEvent e)
+  // {
+    // try
+    // {
+    // frame.setClosed(true);
+    // } catch (Exception ex)
+    // {
+    // }
+  // }
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    cancelled = false;
+    dialog.setVisible(false);
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    cancelled = true;
+    dialog.setVisible(false);
+  }
+
+  @Override
+  public boolean isExportHiddenSequences()
+  {
+    return chkHiddenSeqs.isSelected();
+  }
+
+  @Override
+  public boolean isExportHiddenColumns()
+  {
+    return chkHiddenCols.isSelected();
+  }
+
+  @Override
+  public boolean isExportAnnotations()
+  {
+    return chkExportAnnots.isSelected();
+  }
+
+  @Override
+  public boolean isExportFeatures()
+  {
+    return chkExportFeats.isSelected();
+  }
+
+  @Override
+  public boolean isExportGroups()
+  {
+    return chkExportGrps.isSelected();
+  }
+
+  @Override
+  public boolean isCancelled()
+  {
+    return cancelled;
+  }
+
+}

diff --git a/src/jalview/jbgui/GAlignExportSettings.java b/src/jalview/jbgui/GAlignExportSettings.java
new file mode 100644 (file)
index 0000000..2583b6b
--- /dev/null
+++ b/src/jalview/jbgui/GAlignExportSettings.java
@@ -0,0 +1,146 @@
+package jalview.jbgui;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JPanel;
+
+@SuppressWarnings("serial")
+public abstract class GAlignExportSettings extends JPanel
+{
+  protected JPanel hiddenRegionConfPanel = new JPanel();
+
+  protected JPanel complexExportPanel = new JPanel();
+
+  protected JPanel optionsPanel = new JPanel();
+
+  protected JPanel actionPanel = new JPanel();
+
+  protected BorderLayout hiddenRegionLayout = new BorderLayout();
+
+  protected BorderLayout complexExportLayout = new BorderLayout();
+
+  protected BorderLayout mainLayout = new BorderLayout();
+
+  protected JCheckBox chkAll = new JCheckBox("Check All");
+
+  protected JCheckBox chkHiddenSeqs = new JCheckBox(
+          "Export Hidden Sequences");
+
+  protected JCheckBox chkHiddenCols = new JCheckBox("Export Hidden Columns");
+
+  protected JCheckBox chkExportAnnots = new JCheckBox("Export Annotations");
+
+  protected JCheckBox chkExportFeats = new JCheckBox("Export Features");
+
+  protected JCheckBox chkExportGrps = new JCheckBox("Export Groups");
+
+  JButton btnOk = new JButton("Ok");
+
+  JButton btnCancel = new JButton("Cancel");
+
+  private boolean hasHiddenSeq, hasHiddenCols, isComplexAlignFile;
+
+  boolean isComplexFormat = false;
+
+  public GAlignExportSettings(boolean hasHiddenSeq, boolean hasHiddenCols,
+          String alignFileFormat)
+  {
+    this.hasHiddenSeq = hasHiddenSeq;
+    this.hasHiddenCols = hasHiddenCols;
+    String[] complexFormats =
+    { "JSON", "HTML" };
+
+    for (String format : complexFormats)
+    {
+      if (format.equalsIgnoreCase(alignFileFormat))
+      {
+        this.isComplexAlignFile = true;
+        break;
+      }
+    }
+
+    init();
+  }
+
+  public void init()
+  {
+    hiddenRegionConfPanel.setLayout(hiddenRegionLayout);
+    complexExportPanel.setLayout(complexExportLayout);
+    setLayout(mainLayout);
+
+    chkAll.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        checkAllAction();
+      }
+    });
+
+    btnOk.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+
+    btnCancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+
+    hiddenRegionConfPanel.add(chkAll, BorderLayout.NORTH);
+    hiddenRegionConfPanel.add(chkHiddenSeqs, BorderLayout.CENTER);
+    hiddenRegionConfPanel.add(chkHiddenCols, BorderLayout.SOUTH);
+    chkHiddenSeqs.setEnabled(hasHiddenSeq);
+    chkHiddenCols.setEnabled(hasHiddenCols);
+
+    complexExportPanel.add(chkExportAnnots, BorderLayout.NORTH);
+    complexExportPanel.add(chkExportFeats, BorderLayout.CENTER);
+    complexExportPanel.add(chkExportGrps, BorderLayout.SOUTH);
+
+    if (hasHiddenSeq || hasHiddenCols)
+    {
+      optionsPanel.add(hiddenRegionConfPanel);
+    }
+
+    if (isComplexAlignFile)
+    {
+      optionsPanel.add(complexExportPanel);
+    }
+    actionPanel.add(btnCancel);
+    actionPanel.add(btnOk);
+
+    add(optionsPanel, BorderLayout.NORTH);
+    add(actionPanel, BorderLayout.SOUTH);
+
+  }
+
+
+  
+  private void checkAllAction()
+  {
+    boolean isSelected = chkAll.isSelected();
+    chkHiddenSeqs.setSelected(chkHiddenSeqs.isEnabled() && isSelected);
+    chkHiddenCols.setSelected(chkHiddenCols.isEnabled() && isSelected);
+    chkExportAnnots.setSelected(isComplexAlignFile
+            && chkExportAnnots.isEnabled() && isSelected);
+    chkExportFeats.setSelected(isComplexAlignFile
+            && chkExportFeats.isEnabled() && isSelected);
+    chkExportGrps.setSelected(isComplexAlignFile
+            && chkExportGrps.isEnabled() && isSelected);
+  }
+
+  public abstract void ok_actionPerformed(ActionEvent e);
+
+  public abstract void cancel_actionPerformed(ActionEvent e);
+}