Merge branch 'patch/JAL-2197_jpredforjnets' into develop

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 8e69134..175b171 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -104,7 +104,6 @@ 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;
@@ -221,6 +220,7 @@ 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,
@@ -357,14 +357,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * 
    * @param file
    *          file URL, content, or other resolvable path
-   * @param paste
+   * @param sourceType
    *          is protocol for accessing data referred to by file
    * @param autoenabledisplay
    *          when true, display features flag will be automatically enabled if
    *          features are loaded
    * @return true if data parsed as a features file
    */
-  public boolean parseFeaturesFile(String file, DataSourceType paste,
+  public boolean parseFeaturesFile(String file, DataSourceType sourceType,
           boolean autoenabledisplay)
   {
     boolean featuresFile = false;
@@ -374,7 +374,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               .getFeatureRenderer().getFeatureColours();
       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
               "relaxedidmatch", false);
-      featuresFile = new FeaturesFile(file, paste).parse(
+      featuresFile = new FeaturesFile(file, sourceType).parse(
               viewport.getAlignment(), colours, true, relaxedIdMatching);
     } catch (Exception ex)
     {
@@ -704,9 +704,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.getColumnSelection() != null
-              && viewport.getColumnSelection().getSelected() != null && viewport
-              .getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns()
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -734,8 +732,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         hide = true;
         viewport.hideAllSelectedSeqs();
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
-              .size() > 0))
+      else if (!(toggleCols && viewport.hasSelectedColumns()))
       {
         viewport.showAllHiddenSeqs();
       }
@@ -743,7 +740,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (toggleCols)
     {
-      if (viewport.getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns())
       {
         viewport.hideSelectedColumns();
         if (!toggleSeqs)
@@ -930,11 +927,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
     {
       for (AlignmentAnnotation aa : alignPanel.getAlignment()
-            .getAlignmentAnnotation())
-    {
-      boolean visible = (aa.sequenceRef == null ? showForAlignment
-              : showForSequences);
-      aa.visible = visible;
+              .getAlignmentAnnotation())
+      {
+        boolean visible = (aa.sequenceRef == null ? showForAlignment
+                : showForSequences);
+        aa.visible = visible;
       }
     }
     alignPanel.validateAnnotationDimensions(true);
@@ -1419,9 +1416,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(viewport
-              .getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printJalviewFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols());
     }
     else
     {
@@ -1484,10 +1480,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
     }
 
-    if (viewport.applet.getParameter("jnetfile") != null)
+    if (viewport.applet.getParameter("jnetfile") != null
+            || viewport.applet.getParameter("jpredfile") != null)
     {
       url.append("&annotations=");
-      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+      url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
+              .getParameter("jnetfile") : viewport.applet
+              .getParameter("jpredfile")));
     }
 
     if (viewport.applet.getParameter("defaultColour") != null)
@@ -2235,7 +2234,10 @@ 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();
   }
@@ -2252,7 +2254,10 @@ 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();
   }
@@ -3234,11 +3239,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     Menu outputTextboxMenu = new Menu(
             MessageManager.getString("label.out_to_textbox"));
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats(true))
     {
-
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(ff);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -3512,10 +3515,10 @@ 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"));
@@ -4024,12 +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<String, String>());
-        }
-        pdbentry.getProperty().put("protocol", protocol.toString());
+        pdbentry.setProperty("protocol", protocol);
         toaddpdb.addPDBId(pdbentry);
         alignPanel.getStructureSelectionManager()
                 .registerPDBEntry(pdbentry);
@@ -4079,7 +4077,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     if (protocol == null)
     {
-      String sourceType = pdb.getProperty().get("protocol");
+      String sourceType = (String) pdb.getProperty("protocol");
       try
       {
         protocol = DataSourceType.valueOf(sourceType);