Merge branch 'feature/JAL-2909bamfiles_features' into features/JAL-2909_bamImport2_11

[jalview.git] / src / jalview / gui / BamFileOptionsChooser.java

diff --git a/src/jalview/gui/BamFileOptionsChooser.java b/src/jalview/gui/BamFileOptionsChooser.java
new file mode 100644 (file)
index 0000000..f456319
--- /dev/null
+++ b/src/jalview/gui/BamFileOptionsChooser.java
@@ -0,0 +1,125 @@
+/*
+ * 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.gui;
+
+import jalview.io.AlignmentFileReaderI;
+import jalview.io.BamFile;
+import jalview.util.MessageManager;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.util.Arrays;
+
+import javax.swing.BorderFactory;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+/**
+ * A dialog where a user can choose import options for a bam file
+ */
+public class BamFileOptionsChooser extends JPanel
+{
+
+  // text field for start of range
+  // JFormattedTextField startRange = new JFormattedTextField(
+  // new NumberFormatter(NumberFormat.getIntegerInstance()));
+
+  // text field for end of range
+  // JFormattedTextField endRange = new JFormattedTextField(
+  // new NumberFormatter(NumberFormat.getIntegerInstance()));
+
+  JTextField startRange = new JTextField(10);
+
+  JTextField endRange = new JTextField(10);
+
+  // combo box for chromosome list
+  JComboBox<String> chroCombo;
+
+  public BamFileOptionsChooser(AlignmentFileReaderI source)
+  {
+    Object[] preprocessResult = source.preprocess();
+    String[] chromosomes = Arrays.copyOf(preprocessResult,
+            preprocessResult.length, String[].class);
+
+    setLayout(new GridBagLayout());
+    GridBagConstraints c = new GridBagConstraints();
+
+    setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));
+
+    // set up chromosome input
+    JLabel chroLabel = new JLabel(
+            MessageManager.getString("label.bam_chromosome"));
+    chroCombo = new JComboBox<>(chromosomes);
+    
+    // set up region input
+    JPanel range = new JPanel();
+    JLabel rangeLabel = new JLabel(
+            MessageManager.getString("label.bam_range"));
+    startRange.setColumns(8);
+    endRange.setColumns(8);
+
+    JLabel rangeSep = new JLabel("-");
+    range.add(startRange);
+    range.add(rangeSep);
+    range.add(endRange);
+
+    // chromosome label top left
+    c.gridx = 0;
+    c.gridy = 0;
+    c.anchor = GridBagConstraints.WEST;
+    c.fill = GridBagConstraints.NONE;
+    this.add(chroLabel, c);
+
+    // chromosome combo top right
+    c.gridx = 1;
+    c.weightx = 1;
+    c.anchor = GridBagConstraints.WEST;
+    c.fill = GridBagConstraints.HORIZONTAL;
+    this.add(chroCombo, c);
+
+    // region label mid left
+    c.gridx = 0;
+    c.gridy = 1;
+    c.anchor = GridBagConstraints.WEST;
+    c.fill = GridBagConstraints.NONE;
+    this.add(rangeLabel, c);
+
+    // region input mid right
+    c.gridx = 1;
+    c.weightx = 1;
+    c.anchor = GridBagConstraints.WEST;
+    c.fill = GridBagConstraints.HORIZONTAL;
+    this.add(range, c);
+  }
+
+  public void update(AlignmentFileReaderI source)
+  {
+
+    int start = Integer.parseInt(startRange.getText());
+    int end = Integer.parseInt(endRange.getText());
+    ((BamFile) source).setOptions((String) chroCombo.getSelectedItem(),
+            start, end);
+
+  }
+
+}