JAL-2422 pull up refactoring in preparation for ChimeraX subclasses

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 41a8d5e..846000a 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -106,6 +106,7 @@ import java.awt.event.KeyListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Arrays;
@@ -343,7 +344,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     createAlignFrameWindow(embedded);
     validate();
     alignPanel.adjustAnnotationHeight();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   public AlignViewport getAlignViewport()
@@ -415,7 +416,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         viewport.featureSettings.refreshTable();
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       statusBar.setText(MessageManager
               .getString("label.successfully_added_features_alignment"));
     }
@@ -691,7 +692,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       break;
 
     }
-    alignPanel.paintAlignment(true);
+    // TODO: repaint flags set only if the keystroke warrants it
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -917,7 +919,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       applyAutoAnnotationSettings_actionPerformed();
     }
-    alignPanel.paintAlignment(true);
+    // TODO: repaint flags set only if warranted
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -1094,7 +1097,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == invertColSel)
     {
       viewport.invertColumnSelection();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(false, false);
       viewport.sendSelection();
     }
     else if (source == remove2LeftMenuItem)
@@ -1128,34 +1131,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == showColumns)
     {
       viewport.showAllHiddenColumns();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == showSeqs)
     {
       viewport.showAllHiddenSeqs();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       // uncomment if we want to slave sequence selections in split frame
       // viewport.sendSelection();
     }
     else if (source == hideColumns)
     {
       viewport.hideSelectedColumns();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == hideSequences
             && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       // uncomment if we want to slave sequence selections in split frame
       // viewport.sendSelection();
     }
     else if (source == hideAllButSelection)
     {
       toggleHiddenRegions(false, false);
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == hideAllSelection)
@@ -1164,14 +1167,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.expandColSelection(sg, false);
       viewport.hideAllSelectedSeqs();
       viewport.hideSelectedColumns();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == showAllHidden)
     {
       viewport.showAllHiddenColumns();
       viewport.showAllHiddenSeqs();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == showGroupConsensus)
@@ -1443,15 +1446,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols(),
-              getDisplayedFeatureGroups(), true);
+      features = formatter.printJalviewFormat(
+              viewport.getAlignment().getSequencesArray(),
+              alignPanel.getFeatureRenderer(), true, false);
     }
     else
     {
       features = formatter.printGffFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols(),
-              getDisplayedFeatureGroups(), true);
+              .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
+              false);
     }
 
     if (displayTextbox)
@@ -1568,7 +1571,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     try
     {
       new URL(url);
-      url = URLEncoder.encode(url);
+      url = URLEncoder.encode(url, "UTF-8");
     }
     /*
      * When we finally deprecate 1.1 compatibility, we can start to use
@@ -1581,6 +1584,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       url = viewport.applet.getCodeBase() + url;
     }
+    catch (UnsupportedEncodingException ex)
+    {
+      System.err.println(
+              "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
+                      + url);
+      ex.printStackTrace();
+    }
     return url;
   }
 
@@ -1601,10 +1611,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       System.exit(0);
     }
-    else
+
+    viewport = null;
+    if (alignPanel != null && alignPanel.overviewPanel != null)
     {
+      alignPanel.overviewPanel.dispose();
     }
-    viewport = null;
     alignPanel = null;
     this.dispose();
   }
@@ -1781,7 +1793,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             up ? null : viewport.getHiddenRepSequences(), up);
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
 
     /*
      * Also move cDNA/protein complement sequences
@@ -1793,7 +1805,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               viewport, complement);
       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
               up ? null : complement.getHiddenRepSequences(), up);
-      getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
+      getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
+              false);
     }
   }
 
@@ -1900,7 +1913,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   static StringBuffer copiedSequences;
 
-  static Vector<int[]> copiedHiddenColumns;
+  static HiddenColumns copiedHiddenColumns;
 
   protected void copy_actionPerformed()
   {
@@ -1924,14 +1937,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
     {
-      copiedHiddenColumns = new Vector<>(viewport.getAlignment()
-              .getHiddenColumns().getHiddenColumnsCopy());
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int[] region : copiedHiddenColumns)
-      {
-        region[0] = region[0] - hiddenOffset;
-        region[1] = region[1] - hiddenOffset;
-      }
+      int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+
+      // create new HiddenColumns object with copy of hidden regions
+      // between startRes and endRes, offset by startRes
+      copiedHiddenColumns = new HiddenColumns(
+              viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+              hiddenCutoff, hiddenOffset);
     }
     else
     {
@@ -2000,13 +2013,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     try
     {
-
       if (copiedSequences == null)
       {
         return;
       }
 
-      StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+      StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+              "\t");
       Vector seqs = new Vector();
       while (st.hasMoreElements())
       {
@@ -2038,14 +2051,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
                 viewport.applet, newtitle, false);
-        if (copiedHiddenColumns != null)
-        {
-          for (int i = 0; i < copiedHiddenColumns.size(); i++)
-          {
-            int[] region = copiedHiddenColumns.elementAt(i);
-            af.viewport.hideColumns(region[0], region[1]);
-          }
-        }
+        af.viewport.setHiddenColumns(copiedHiddenColumns);
 
         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
                 frameHeight);
@@ -2226,7 +2232,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -2263,7 +2269,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
     // updating.
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2283,7 +2289,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
     // updating.
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2303,7 +2309,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void invertColSel_actionPerformed()
   {
     viewport.invertColumnSelection();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2595,19 +2601,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     viewport.setShowJVSuffix(seqLimits.getState());
     alignPanel.fontChanged();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   protected void colourTextMenuItem_actionPerformed()
   {
     viewport.setColourText(colourTextMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   protected void displayNonconservedMenuItem_actionPerformed()
   {
     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   protected void wrapMenuItem_actionPerformed()
@@ -2617,7 +2623,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     scaleAbove.setEnabled(wrapMenuItem.getState());
     scaleLeft.setEnabled(wrapMenuItem.getState());
     scaleRight.setEnabled(wrapMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void overviewMenuItem_actionPerformed()
@@ -2660,7 +2666,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     viewport.setGlobalColourScheme(cs);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   protected void modifyPID_actionPerformed()
@@ -2735,7 +2741,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void sortIDMenuItem_actionPerformed()
@@ -2744,7 +2750,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(
             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void sortLengthMenuItem_actionPerformed()
@@ -2753,7 +2759,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     AlignmentSorter.sortByLength(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void sortGroupMenuItem_actionPerformed()
@@ -2762,7 +2768,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
 
   }
 
@@ -2802,7 +2808,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           current.insertCharAt(Width - 1, viewport.getGapCharacter());
         }
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(false, false);
     }
 
     if ((viewport.getSelectionGroup() != null
@@ -2866,7 +2872,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           current.insertCharAt(Width - 1, viewport.getGapCharacter());
         }
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(false, false);
 
     }
 
@@ -2919,7 +2925,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     addHistoryItem(new OrderCommand(MessageManager
             .formatMessage("label.order_by_params", new String[]
             { title }), oldOrder, viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -2977,7 +2983,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       addHistoryItem(new OrderCommand(undoname, oldOrder,
               viewport.getAlignment()));
     }
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     return true;
   }
 
@@ -3956,7 +3962,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * without an additional javascript library to exchange messages between the
    * distinct applets. See http://issues.jalview.org/browse/JAL-621
    * 
-   * @param viewer
+   * @param jmolViewer
    *          JmolViewer instance
    * @param sequenceIds
    *          - sequence Ids to search for associations