From 670c6ccb4d070850b8ba3af2a99f600459a61bbe Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 7 Oct 2013 16:59:52 +0100
Subject: [PATCH] JAL-1385 Alignment view controller logic implementation and
 API

---
 src/jalview/api/AlignViewControllerI.java       |   24 ++++++
 src/jalview/controller/AlignViewController.java |  100 +++++++++++++++++++++++
 2 files changed, 124 insertions(+)
 create mode 100644 src/jalview/api/AlignViewControllerI.java
 create mode 100644 src/jalview/controller/AlignViewController.java

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
new file mode 100644
index 0000000..fc63fd6
--- /dev/null
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -0,0 +1,24 @@
+package jalview.api;
+
+/**
+ * prototype abstract controller for a Jalview alignment view
+ * @author jimp
+ * 
+ * All operations should return true if the view has changed as a result of the operation
+ * @param <ViewportI>
+ *
+ */
+public interface AlignViewControllerI<ViewportI>
+{
+
+  public boolean makeGroupsFromSelection();
+
+  public boolean createGroup();
+
+  public boolean unGroup();
+
+  public boolean deleteGroups();
+
+  public void setViewportAndAlignmentPanel(AlignViewportI viewport, AlignmentViewPanel alignPanel);
+
+}
diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
new file mode 100644
index 0000000..16e8cdd
--- /dev/null
+++ b/src/jalview/controller/AlignViewController.java
@@ -0,0 +1,100 @@
+package jalview.controller;
+
+import java.awt.Color;
+
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+public class AlignViewController implements AlignViewControllerI
+{
+  AlignViewportI viewport=null;
+  AlignmentViewPanel alignPanel=null;
+  @Override
+  protected void finalize() throws Throwable {
+    viewport = null;
+    alignPanel = null;
+  };
+  
+  public AlignViewController(AlignViewportI viewport,
+          AlignmentViewPanel alignPanel)
+  {
+    this.viewport=viewport;
+    this.alignPanel = alignPanel;
+  }
+  @Override
+  public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
+  {
+    this.alignPanel = alignPanel;
+    this.viewport = viewport;
+    
+  }
+  @Override
+  public boolean makeGroupsFromSelection()
+  {
+
+    if (viewport.getSelectionGroup() != null)
+    {
+      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+              viewport.getSequenceSelection(),
+              viewport.getAlignmentView(true).getSequenceStrings(
+                      viewport.getGapCharacter()), viewport.getAlignment()
+                      .getGroups());
+      viewport.getAlignment().deleteAllGroups();
+      viewport.clearSequenceColours();
+      viewport.setSelectionGroup(null);
+      // set view properties for each group
+      for (int g = 0; g < gps.length; g++)
+      {
+        // gps[g].setShowunconserved(viewport.getShowUnconserved());
+        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+        viewport.getAlignment().addGroup(gps[g]);
+        Color col = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
+        col = col.brighter();
+        for (SequenceI sq : gps[g].getSequences(null))
+          viewport.setSequenceColour(sq, col);
+      }
+      return true;
+    }
+    return false;
+}
+  @Override
+  public boolean createGroup()
+  {
+
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg!=null)
+    {
+        viewport.getAlignment().addGroup(sg);
+        return true;
+      } 
+    return false;
+  }
+  @Override
+  public boolean unGroup()
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg!=null)
+    {
+        viewport.getAlignment().deleteGroup(sg);
+        return true;
+    }
+    return false;
+  }
+  @Override
+  public boolean deleteGroups()
+  {
+    if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
+    {
+    viewport.getAlignment().deleteAllGroups();
+    viewport.clearSequenceColours();
+    viewport.setSelectionGroup(null);
+    return true;
+    }
+    return false;
+  }
+    
+  }
-- 
1.7.10.2