From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Thu, 24 Aug 2017 09:21:15 +0000 (+0100)
Subject: JAL-2629 remove sequence and group HMMER options
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6ebc0175847b996abb1fa594492a5c9d23230276;p=jalview.git

JAL-2629 remove sequence and group HMMER options
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 179880e..7d124da 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -25,6 +25,7 @@ import jalview.analysis.Conservation;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -697,8 +698,8 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       getInformation();
     }
-    information.label = "Information for " + getName();
-    information.description = "Percent Identity";
+    information.description = MessageManager
+            .getString("label.information_description");
     informationData = cnsns;
     // preserve width if already set
     int aWidth = (information.annotations != null)
@@ -708,7 +709,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     information.annotations = null;
     information.annotations = new Annotation[aWidth]; // should be alignment
                                                       // width
-
+    information.calcId = "HMM";
     AAFrequency.completeInformation(information, cnsns, startRes,
             endRes + 1, ignoreBelowBackground, showSequenceLogo, nseq); // TODO:
                                                                         // setting
@@ -1188,6 +1189,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       information.groupRef = this;
       information.label = getName() + "_HMM";
       information.description = "Information content, measured in bits";
+      information.calcId = "HMM";
     }
     return information;
   }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 97ce501..3fc86d0 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -39,8 +39,6 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
-import jalview.hmmer.HMMAlignThread;
-import jalview.hmmer.HMMBuildThread;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
@@ -160,7 +158,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   JMenuItem sequenceFeature = new JMenuItem();
 
-  JMenuItem hmmBuildGroup = new JMenuItem();
 
   JMenuItem textColour = new JMenuItem();
 
@@ -371,21 +368,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
           }
         });
         add(selectHMM);
-
-        JMenuItem hmmAlign = new JCheckBoxMenuItem();
-        hmmAlign.setText(MessageManager.getString("label.hmmalign"));
-        hmmAlign.addActionListener(new ActionListener()
-        {
-
-          @Override
-          public void actionPerformed(ActionEvent e)
-          {
-            hmmAlign_actionPerformed(e);
-          }
-        });
-        add(hmmAlign);
       }
 
+
       if (ap.av.getSelectionGroup() != null
               && ap.av.getSelectionGroup().getSize() > 1)
       {
@@ -1167,15 +1152,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         sequenceFeature_actionPerformed();
       }
     });
-    hmmBuildGroup.setText(MessageManager.getString("label.group_hmmbuild"));
-    hmmBuildGroup.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmBuildGroup_actionPerformed();
-      }
-    });
     jMenu1.setText(MessageManager.getString("label.group"));
     pdbStructureDialog.setText(
             MessageManager.getString("label.show_pdbstruct_dialog"));
@@ -1285,12 +1261,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     jMenu1.add(displayNonconserved);
   }
 
-  protected void hmmBuildGroup_actionPerformed()
-  {
-    new Thread(new HMMBuildThread(ap.alignFrame)).start();
-    ap.repaint();
-
-  }
 
   protected void selectHMM_actionPerformed(ActionEvent e)
   {
@@ -1298,13 +1268,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     ap.alignFrame.setSelectedHMMSequence(hmm);
   }
 
-  protected void hmmAlign_actionPerformed(ActionEvent e)
-  {
-    ap.alignFrame.setSelectedHMMSequence(this.sequence);
-    new Thread(new HMMAlignThread(ap.alignFrame, true)).start();
-    ap.repaint();
-  }
-
   /**
    * Constructs the entries for the colour menu
    */