Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b218e7a..6302f69 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,11 +63,11 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.hmmer.HMMAlignThread;
-import jalview.hmmer.HMMBuildThread;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
 import jalview.hmmer.HMMERParamStore;
 import jalview.hmmer.HMMERPreset;
-import jalview.hmmer.HMMSearchThread;
+import jalview.hmmer.HMMSearch;
 import jalview.hmmer.HmmerCommand;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
@@ -1037,7 +1037,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             args);
     if (params.showRunDialog())
     {
-      new Thread(new HMMBuildThread(this, params.getJobParams())).start();
+      new Thread(new HMMBuild(this, params.getJobParams())).start();
     }
     alignPanel.repaint();
 
@@ -1057,7 +1057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             args);
     if (params.showRunDialog())
     {
-      new Thread(new HMMAlignThread(this, params.getJobParams()))
+      new Thread(new HMMAlign(this, params.getJobParams()))
             .start();
     }
     alignPanel.repaint();
@@ -1077,7 +1077,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             args);
     if (params.showRunDialog())
     {
-      new Thread(new HMMSearchThread(this, params.getJobParams()))
+      new Thread(new HMMSearch(this, params.getJobParams()))
             .start();
     }
     alignPanel.repaint();
@@ -1090,7 +1090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    new Thread(new HMMBuildThread(this, null))
+    new Thread(new HMMBuild(this, null))
             .start();
   }
 
@@ -1101,7 +1101,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    new Thread(new HMMAlignThread(this, null)).start();
+    new Thread(new HMMAlign(this, null)).start();
   }
 
   @Override
@@ -1111,7 +1111,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    new Thread(new HMMSearchThread(this, null)).start();
+    new Thread(new HMMSearch(this, null)).start();
   }
 
   /**
@@ -2090,25 +2090,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<>();
-
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
-      ArrayList<int[]> hiddenRegions = viewport.getAlignment()
-              .getHiddenColumns().getHiddenColumnsCopy();
-      for (int[] region : hiddenRegions)
 
-      {
-        if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
-        {
-          hiddenColumns
-                  .add(new int[]
-                  { region[0] - hiddenOffset, region[1] - hiddenOffset });
-        }
-      }
+      // create new HiddenColumns object with copy of hidden regions
+      // between startRes and endRes, offset by startRes
+      hiddenColumns = new HiddenColumns(
+              viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+              hiddenCutoff, hiddenOffset);
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs,
@@ -2445,11 +2437,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (Desktop.jalviewClipboard != null
                 && Desktop.jalviewClipboard[2] != null)
         {
-          List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
-          for (int[] region : hc)
-          {
-            af.viewport.hideColumns(region[0], region[1]);
-          }
+          HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+          af.viewport.setHiddenColumns(hc);
         }
 
         // >>>This is a fix for the moment, until a better solution is
@@ -2503,11 +2492,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Desktop.jalviewClipboard != null
               && Desktop.jalviewClipboard[2] != null)
       {
-        List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
-        for (int region[] : hc)
-        {
-          af.viewport.hideColumns(region[0], region[1]);
-        }
+        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+        af.viewport.setHiddenColumns(hc);
       }
 
       // >>>This is a fix for the moment, until a better solution is
@@ -4878,11 +4864,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             new JnetAnnotationMaker();
             JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
-            SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
-            viewport.getAlignment().setSeqrep(repseq);
-            HiddenColumns cs = new HiddenColumns();
-            cs.hideInsertionsFor(repseq);
-            viewport.getAlignment().setHiddenColumns(cs);
+            viewport.getAlignment().setupJPredAlignment();
             isAnnotation = true;
           }
           // else if (IdentifyFile.FeaturesFile.equals(format))
@@ -5103,14 +5085,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             MessageManager.getString("option.trim_retrieved_seqs"));
     trimrs.setToolTipText(
             MessageManager.getString("label.trim_retrieved_sequences"));
-    trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+    trimrs.setSelected(
+            Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
     trimrs.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         trimrs.setSelected(trimrs.isSelected());
-        Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+        Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
                 Boolean.valueOf(trimrs.isSelected()).toString());
       };
     });