JAL-2050 only hide introns if exons are present! Removed 'hide introns'

checkbox from Preferences gui

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 9a064b1..05505a4 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -608,7 +608,6 @@ label.automatically_set_id_width = Automatically set ID width
 label.figure_id_column_width = Figure ID column width
 label.use_modeller_output = Use Modeller Output
 label.wrap_alignment = Wrap Alignment
-label.hide_introns = Hide Introns
 label.right_align_ids = Right Align Ids
 label.sequence_name_italics = Italic Sequence Ids
 label.open_overview = Open Overview
@@ -1259,7 +1258,6 @@ label.biojs_html_export = BioJS
 label.scale_as_cdna = Scale protein residues to codons
 label.scale_protein_to_cdna = Scale Protein to cDNA
 label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views
-label.hide_introns_tip = Hide intron columns after fetching genomic sequences
 info.select_annotation_row = Select Annotation Row
 info.enter_search_text_here = Enter Search Text Here
 info.enter_search_text_to_enable = Enter Search Text to Enable

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8b33deb..c7e1332 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -88,8 +88,6 @@ public class Preferences extends GPreferences
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 
-  public static final String HIDE_INTRONS = "HIDE_INTRONS";
-
   private static final int MIN_FONT_SIZE = 1;
 
   private static final int MAX_FONT_SIZE = 30;
@@ -177,11 +175,11 @@ public class Preferences extends GPreferences
     dasTab.add(dasSource, BorderLayout.CENTER);
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
-    int width = 500, height = 470;
+    int width = 500, height = 450;
     if (new jalview.util.Platform().isAMac())
     {
       width = 570;
-      height = 500;
+      height = 480;
     }
 
     Desktop.addInternalFrame(frame,
@@ -243,7 +241,6 @@ public class Preferences extends GPreferences
     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
-    hideIntrons.setSelected(Cache.getDefault(HIDE_INTRONS, true));
 
     gapSymbolCB.addItem("-");
     gapSymbolCB.addItem(".");
@@ -461,8 +458,6 @@ public class Preferences extends GPreferences
 
     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
             Boolean.toString(wrap.isSelected()));
-    Cache.applicationProperties.setProperty(HIDE_INTRONS,
-            Boolean.toString(hideIntrons.isSelected()));
 
     Cache.applicationProperties.setProperty("STARTUP_FILE",
             startupFileTextfield.getText());

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index a5f218e..eb33ce7 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -840,9 +840,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
-          af.avc.markColumnsContainingFeatures(true, false, false,
-                  SequenceOntologyI.EXON);
-          af.getViewport().hideSelectedColumns();
+          hideIntronsIfPresent(af);
         }
 
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
@@ -867,6 +865,25 @@ public class SequenceFetcher extends JPanel implements Runnable
     return al;
   }
 
+  /**
+   * Hide columns not containing 'exon' features, provided there are exon
+   * features on the alignment
+   * 
+   * @param af
+   */
+  public void hideIntronsIfPresent(AlignFrame af)
+  {
+    boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
+            false,
+            SequenceOntologyI.EXON);
+    if (hasExons)
+    {
+      af.avc.markColumnsContainingFeatures(true, false, true,
+              SequenceOntologyI.EXON);
+      af.getViewport().hideSelectedColumns();
+    }
+  }
+
   void showErrorMessage(final String error)
   {
     resetDialog();

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 0aafe50..b5c1804 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -110,8 +110,6 @@ public class GPreferences extends JPanel
 
   protected JCheckBox wrap = new JCheckBox();
 
-  protected JCheckBox hideIntrons = new JCheckBox();
-
   protected JComboBox<String> sortby = new JComboBox<String>();
 
   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
@@ -1151,7 +1149,7 @@ public class GPreferences extends JPanel
     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
     startupCheckbox.setSelected(true);
     startupFileTextfield.setFont(LABEL_FONT);
-    startupFileTextfield.setBounds(new Rectangle(173, 328, 330, 20));
+    startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
     startupFileTextfield.addMouseListener(new MouseAdapter()
     {
       @Override
@@ -1165,19 +1163,19 @@ public class GPreferences extends JPanel
     });
 
     sortby.setFont(LABEL_FONT);
-    sortby.setBounds(new Rectangle(172, 280, 155, 20));
+    sortby.setBounds(new Rectangle(172, 260, 155, 21));
     JLabel sortLabel = new JLabel();
     sortLabel.setFont(LABEL_FONT);
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     sortLabel.setText(MessageManager.getString("label.sort_by"));
     sortAnnBy.setFont(LABEL_FONT);
-    sortAnnBy.setBounds(new Rectangle(172, 305, 110, 20));
+    sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
     JLabel sortAnnLabel = new JLabel();
     sortAnnLabel.setFont(LABEL_FONT);
     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
     sortAutocalc.setFont(LABEL_FONT);
-    sortAutocalc.setBounds(new Rectangle(290, 305, 165, 20));
+    sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
 
     JPanel annsettingsPanel = new JPanel();
     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
@@ -1221,12 +1219,6 @@ public class GPreferences extends JPanel
     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
     wrap.setText(MessageManager.getString("label.wrap_alignment"));
-    hideIntrons.setFont(LABEL_FONT);
-    hideIntrons.setHorizontalAlignment(SwingConstants.TRAILING);
-    hideIntrons.setHorizontalTextPosition(SwingConstants.LEADING);
-    hideIntrons.setText(MessageManager.getString("label.hide_introns"));
-    hideIntrons.setToolTipText(MessageManager
-            .getString("label.hide_introns_tip"));
     rightAlign.setFont(LABEL_FONT);
     rightAlign.setForeground(Color.black);
     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -1244,8 +1236,8 @@ public class GPreferences extends JPanel
     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
     openoverv.setText(MessageManager.getString(("label.open_overview")));
     JPanel jPanel2 = new JPanel();
-    jPanel2.setBounds(new Rectangle(7, 17, 158, 330));
-    jPanel2.setLayout(new GridLayout(15, 1));
+    jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
+    jPanel2.setLayout(new GridLayout(14, 1));
     jPanel2.add(fullScreen);
     jPanel2.add(openoverv);
     jPanel2.add(seqLimit);
@@ -1257,7 +1249,6 @@ public class GPreferences extends JPanel
     jPanel2.add(scaleProteinToCdna);
     jPanel2.add(gapLabel);
     jPanel2.add(wrap);
-    jPanel2.add(hideIntrons);
     jPanel2.add(sortLabel);
     jPanel2.add(sortAnnLabel);
     jPanel2.add(startupCheckbox);