JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

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

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 80f03a1..15e269c 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -34,11 +34,12 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
-public class IdPanel extends Panel implements MouseListener,
-        MouseMotionListener
+public class IdPanel extends Panel
+        implements MouseListener, MouseMotionListener
 {
 
   protected IdCanvas idCanvas;
@@ -55,11 +56,11 @@ public class IdPanel extends Panel implements MouseListener,
 
   UrlProviderI urlProvider = null;
 
-  public IdPanel(AlignViewport av, AlignmentPanel parent)
+  public IdPanel(AlignViewport viewport, AlignmentPanel parent)
   {
-    this.av = av;
+    this.av = viewport;
     alignPanel = parent;
-    idCanvas = new IdCanvas(av);
+    idCanvas = new IdCanvas(viewport);
     setLayout(new BorderLayout());
     add(idCanvas, BorderLayout.CENTER);
     idCanvas.addMouseListener(this);
@@ -69,13 +70,13 @@ public class IdPanel extends Panel implements MouseListener,
     // TODO: add in group link parameter
 
     // make a list of label,url pairs
-    HashMap<String, String> urlList = new HashMap<String, String>();
-    if (av.applet != null)
+    HashMap<String, String> urlList = new HashMap<>();
+    if (viewport.applet != null)
     {
       for (int i = 1; i < 10; i++)
       {
-        label = av.applet.getParameter("linkLabel_" + i);
-        url = av.applet.getParameter("linkURL_" + i);
+        label = viewport.applet.getParameter("linkLabel_" + i);
+        url = viewport.applet.getParameter("linkURL_" + i);
 
         // only add non-null parameters
         if (label != null)
@@ -87,7 +88,7 @@ public class IdPanel extends Panel implements MouseListener,
       if (!urlList.isEmpty())
       {
         // set default as first entry in list
-        String defaultUrl = av.applet.getParameter("linkLabel_1");
+        String defaultUrl = viewport.applet.getParameter("linkLabel_1");
         UrlProviderFactoryI factory = new AppletUrlProviderFactory(
                 defaultUrl, urlList);
         urlProvider = factory.createUrlProvider();
@@ -168,13 +169,14 @@ public class IdPanel extends Panel implements MouseListener,
     }
     if (tooltip == null)
     {
-      tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString(), idCanvas);
+      tooltip = new Tooltip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+              idCanvas);
     }
     else
     {
-      tooltip.setTip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString());
+      tooltip.setTip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
     }
     tooltiptext = null;
   }
@@ -196,7 +198,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   @Override
@@ -217,6 +219,10 @@ public class IdPanel extends Panel implements MouseListener,
     String id = sq.getName();
 
     // get the default url with the sequence details filled in
+    if (urlProvider == null)
+    {
+      return;
+    }
     String url = urlProvider.getPrimaryUrl(id);
     String target = urlProvider.getPrimaryTarget(id);
     try
@@ -273,7 +279,8 @@ public class IdPanel extends Panel implements MouseListener,
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((e.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
       SequenceI sq = av.getAlignment().getSequenceAt(seq);
 
@@ -281,7 +288,15 @@ public class IdPanel extends Panel implements MouseListener,
        *  build a new links menu based on the current links
        *  and any non-positional features
        */
-      List<String> nlinks = urlProvider.getLinksForMenu();
+      List<String> nlinks;
+      if (urlProvider != null)
+      {
+        nlinks = urlProvider.getLinksForMenu();
+      }
+      else
+      {
+        nlinks = new ArrayList<>();
+      }
 
       for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
       {
@@ -301,8 +316,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || ((!jalview.util.Platform.isControlDown(e) && !e
-                    .isShiftDown()) && av.getSelectionGroup() != null))
+            || ((!jalview.util.Platform.isControlDown(e)
+                    && !e.isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -318,7 +333,7 @@ public class IdPanel extends Panel implements MouseListener,
       selectSeq(seq);
     }
 
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   void selectSeq(int seq)
@@ -351,8 +366,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i == end);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
     }
 
   }
@@ -391,7 +406,7 @@ public class IdPanel extends Panel implements MouseListener,
     if (av.getRanges().getStartSeq() > index
             || av.getRanges().getEndSeq() < index)
     {
-      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -402,9 +417,9 @@ public class IdPanel extends Panel implements MouseListener,
 
     boolean up = true;
 
-    public ScrollThread(boolean up)
+    public ScrollThread(boolean isUp)
     {
-      this.up = up;
+      this.up = isUp;
       start();
     }
 
@@ -419,7 +434,7 @@ public class IdPanel extends Panel implements MouseListener,
       running = true;
       while (running)
       {
-        if (alignPanel.scrollUp(up))
+        if (av.getRanges().scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
           int seq = av.getRanges().getStartSeq();
@@ -444,7 +459,7 @@ public class IdPanel extends Panel implements MouseListener,
           running = false;
         }
 
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, false);
         try
         {
           Thread.sleep(100);