JAL-2196 refactor PDBEntry.getProperty,setProperty,getProperties

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b7e7899..e9e0786 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SequenceStructureBinding;
@@ -101,7 +102,6 @@ import java.net.URLEncoder;
 import java.util.Arrays;
 import java.util.Deque;
 import java.util.HashMap;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
@@ -218,6 +218,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.setColumnSelection(columnSelection);
     }
+    viewport.setScaleAboveWrapped(scaleAbove.getState());
 
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -364,18 +365,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public boolean parseFeaturesFile(String file, String type,
           boolean autoenabledisplay)
   {
-    // TODO: test if importing a features file onto an alignment which already
-    // has features with links overwrites the original links.
-
-    Hashtable featureLinks = new Hashtable();
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
-              .getAlignment(), alignPanel.seqPanel.seqCanvas
-              .getFeatureRenderer().getFeatureColours(), featureLinks,
-              true, viewport.applet.getDefaultParameter("relaxedidmatch",
-                      false));
+      Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
+              .getFeatureRenderer().getFeatureColours();
+      boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
+              "relaxedidmatch", false);
+      featuresFile = new FeaturesFile(file, type).parse(
+              viewport.getAlignment(), colours, true, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -383,10 +381,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (featuresFile)
     {
-      if (featureLinks.size() > 0)
-      {
-        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
-      }
       if (autoenabledisplay)
       {
         viewport.setShowSequenceFeatures(true);
@@ -1406,7 +1400,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return annotation;
   }
 
-  private Map<String, Object> getDisplayedFeatureCols()
+  private Map<String, FeatureColourI> getDisplayedFeatureCols()
   {
     if (alignPanel.getFeatureRenderer() != null
             && viewport.getFeaturesDisplayed() != null)
@@ -1420,15 +1414,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public String outputFeatures(boolean displayTextbox, String format)
   {
     String features;
+    FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = new FeaturesFile().printJalviewFormat(viewport
+      features = formatter.printJalviewFormat(viewport
               .getAlignment().getSequencesArray(),
               getDisplayedFeatureCols());
     }
     else
     {
-      features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+      features = formatter.printGffFormat(viewport.getAlignment()
               .getSequencesArray(), getDisplayedFeatureCols());
     }
 
@@ -2238,7 +2233,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2255,7 +2253,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -3515,10 +3516,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
-            .getString("label.modify_identity_thereshold"));
+            .getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(this);
     modifyConservation.setLabel(MessageManager
-            .getString("label.modify_conservation_thereshold"));
+            .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(this);
     annotationColour.setLabel(MessageManager
             .getString("action.by_annotation"));
@@ -4026,12 +4027,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (needtoadd)
       {
-        // make a note of the access mode and add
-        if (pdbentry.getProperty() == null)
-        {
-          pdbentry.setProperty(new Hashtable());
-        }
-        pdbentry.getProperty().put("protocol", protocol);
+        pdbentry.setProperty("protocol", protocol);
         toaddpdb.addPDBId(pdbentry);
         alignPanel.getStructureSelectionManager()
                 .registerPDBEntry(pdbentry);
@@ -4082,7 +4078,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (protocol == null || protocol.trim().length() == 0
             || protocol.equals("null"))
     {
-      protocol = (String) pdb.getProperty().get("protocol");
+      protocol = (String) pdb.getProperty("protocol");
       if (protocol == null)
       {
         System.err.println("Couldn't work out protocol to open structure: "