Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 66eb053..a5c2e5a 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,7 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -57,11 +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);
@@ -72,12 +71,12 @@ public class IdPanel extends Panel implements MouseListener,
 
     // make a list of label,url pairs
     HashMap<String, String> urlList = new HashMap<String, String>();
-    if (av.applet != null)
+    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)
@@ -89,7 +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();
@@ -106,64 +105,57 @@ public class IdPanel extends Panel implements MouseListener,
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    // look for non-pos features
     StringBuffer tooltiptext = new StringBuffer();
-    if (sequence != null)
+    if (sequence == null)
     {
-      if (sequence.getDescription() != null)
+      return;
+    }
+    if (sequence.getDescription() != null)
+    {
+      tooltiptext.append(sequence.getDescription());
+      tooltiptext.append("\n");
+    }
+
+    for (SequenceFeature sf : sequence.getFeatures()
+            .getNonPositionalFeatures())
+    {
+      boolean nl = false;
+      if (sf.getFeatureGroup() != null)
       {
-        tooltiptext.append(sequence.getDescription());
-        tooltiptext.append("\n");
+        tooltiptext.append(sf.getFeatureGroup());
+        nl = true;
       }
-
-      SequenceFeature sf[] = sequence.getSequenceFeatures();
-      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      if (sf.getType() != null)
       {
-        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
-        {
-          boolean nl = false;
-          if (sf[sl].getFeatureGroup() != null)
-          {
-            tooltiptext.append(sf[sl].getFeatureGroup());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getType() != null)
-          {
-            tooltiptext.append(" ");
-            tooltiptext.append(sf[sl].getType());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getDescription() != null)
-          {
-            tooltiptext.append(" ");
-            tooltiptext.append(sf[sl].getDescription());
-            nl = true;
-          }
-          ;
-          if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
-          {
-            tooltiptext.append(" Score = ");
-            tooltiptext.append(sf[sl].getScore());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
-          {
-            tooltiptext.append(" (");
-            tooltiptext.append(sf[sl].getStatus());
-            tooltiptext.append(")");
-            nl = true;
-          }
-          ;
-          if (nl)
-          {
-            tooltiptext.append("\n");
-          }
-        }
+        tooltiptext.append(" ");
+        tooltiptext.append(sf.getType());
+        nl = true;
+      }
+      if (sf.getDescription() != null)
+      {
+        tooltiptext.append(" ");
+        tooltiptext.append(sf.getDescription());
+        nl = true;
+      }
+      if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+      {
+        tooltiptext.append(" Score = ");
+        tooltiptext.append(sf.getScore());
+        nl = true;
+      }
+      if (sf.getStatus() != null && sf.getStatus().length() > 0)
+      {
+        tooltiptext.append(" (");
+        tooltiptext.append(sf.getStatus());
+        tooltiptext.append(")");
+        nl = true;
+      }
+      if (nl)
+      {
+        tooltiptext.append("\n");
       }
     }
+
     if (tooltiptext.length() == 0)
     {
       // nothing to display - so clear tooltip if one is visible
@@ -288,10 +280,12 @@ public class IdPanel extends Panel implements MouseListener,
 
     if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+      SequenceI sq = av.getAlignment().getSequenceAt(seq);
 
-      // build a new links menu based on the current links + any non-positional
-      // features
+      /*
+       *  build a new links menu based on the current links
+       *  and any non-positional features
+       */
       List<String> nlinks;
       if (urlProvider != null)
       {
@@ -301,17 +295,14 @@ public class IdPanel extends Panel implements MouseListener,
       {
         nlinks = new ArrayList<String>();
       }
-      SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
-      for (int sl = 0; sf != null && sl < sf.length; sl++)
+
+      for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
       {
-        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+        if (sf.links != null)
         {
-          if (sf[sl].links != null && sf[sl].links.size() > 0)
+          for (String link : sf.links)
           {
-            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
-            {
-              nlinks.add(sf[sl].links.elementAt(l));
-            }
+            nlinks.add(link);
           }
         }
       }
@@ -424,9 +415,9 @@ 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();
     }