From 6d1f6d9f50eb9beca568907bd90bda54a133986a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 4 May 2016 16:04:26 +0100
Subject: [PATCH] JAL-2092 hide columns with/without feature

---
 resources/lang/Messages.properties         |    2 +
 src/jalview/appletgui/FeatureSettings.java |   72 ++++++++++++++++++++++++++++
 src/jalview/gui/FeatureSettings.java       |   24 +++++++++-
 3 files changed, 96 insertions(+), 2 deletions(-)

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index be5f040..8dac5c6 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -801,6 +801,8 @@ label.wswublast_client_credits = To display sequence features an exact Uniprot i
 label.blasting_for_unidentified_sequence = BLASTing for unidentified sequences
 label.select_columns_containing = Select columns containing
 label.select_columns_not_containing = Select columns that do not contain
+label.hide_columns_containing = Hide columns containing
+label.hide_columns_not_containing = Hide columns that do not contain
 option.trim_retrieved_seqs = Trim retrieved sequences
 label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
 label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index bef6437..7ae318c 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -222,6 +222,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     });
     men.add(dens);
+
     if (minmax != null)
     {
       final float[][] typeMinMax = minmax.get(type);
@@ -267,6 +268,57 @@ public class FeatureSettings extends Panel implements ItemListener,
         });
       }
     }
+
+    MenuItem selectContaining = new MenuItem(
+            MessageManager.getString("label.select_columns_containing"));
+    selectContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+                false, type);
+      }
+    });
+    men.add(selectContaining);
+
+    MenuItem selectNotContaining = new MenuItem(
+            MessageManager.getString("label.select_columns_not_containing"));
+    selectNotContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+                false, type);
+      }
+    });
+    men.add(selectNotContaining);
+
+    MenuItem hideContaining = new MenuItem(
+            MessageManager.getString("label.hide_columns_containing"));
+    hideContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideFeatureColumns(type, true);
+      }
+    });
+    men.add(hideContaining);
+
+    MenuItem hideNotContaining = new MenuItem(
+            MessageManager.getString("label.hide_columns_not_containing"));
+    hideNotContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideFeatureColumns(type, false);
+      }
+    });
+    men.add(hideNotContaining);
+
     this.featurePanel.add(men);
     men.show(this.featurePanel, x, y);
   }
@@ -778,4 +830,24 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
   }
 
+  /**
+   * Hide columns containing (or not containing) a given feature type
+   * 
+   * @param type
+   * @param columnsContaining
+   */
+  void hideFeatureColumns(final String type,
+          boolean columnsContaining)
+  {
+    if (ap.alignFrame.avc.markColumnsContainingFeatures(
+            columnsContaining, false, false, type))
+    {
+      if (ap.alignFrame.avc.markColumnsContainingFeatures(
+              !columnsContaining, false, false, type))
+      {
+        ap.alignFrame.viewport.hideSelectedColumns();
+      }
+    }
+  }
+
 }
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6633156..40635c0 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -394,7 +394,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_containing"));
     selCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -406,7 +405,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_not_containing"));
     clearCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -414,8 +412,30 @@ public class FeatureSettings extends JPanel implements
                 false, type);
       }
     });
+    JMenuItem hideCols = new JMenuItem(
+            MessageManager.getString("label.hide_columns_containing"));
+    hideCols.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.hideFeatureColumns(type, true);
+      }
+    });
+    JMenuItem hideOtherCols = new JMenuItem(
+            MessageManager.getString("label.hide_columns_not_containing"));
+    hideOtherCols.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.hideFeatureColumns(type, false);
+      }
+    });
     men.add(selCols);
     men.add(clearCols);
+    men.add(hideCols);
+    men.add(hideOtherCols);
     men.show(table, x, y);
   }
 
-- 
1.7.10.2