JAL-1499 MEGA format, JAL-1421 List<String> url links

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 5dfe581..c86240f 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -35,8 +35,8 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
@@ -196,7 +196,7 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    Vector links = Preferences.sequenceURLLinks;
+    List<String> links = Preferences.getSequenceURLLinks();
     if (links == null || links.size() < 1)
     {
       return;
@@ -210,7 +210,7 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       // DEFAULT LINK IS FIRST IN THE LINK LIST
       // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
-      url = links.elementAt(i++).toString();
+      url = links.get(i++).toString();
       jalview.util.UrlLink urlLink = null;
       try
       {
@@ -252,12 +252,6 @@ public class IdPanel extends JPanel implements MouseListener,
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
   @Override
   public void mouseEntered(MouseEvent e)
   {
@@ -267,12 +261,6 @@ public class IdPanel extends JPanel implements MouseListener,
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
   @Override
   public void mouseExited(MouseEvent e)
   {
@@ -321,7 +309,8 @@ public class IdPanel extends JPanel implements MouseListener,
       Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
       // build a new links menu based on the current links + any non-positional
       // features
-      Vector nlinks = new Vector(Preferences.sequenceURLLinks);
+      List<String> nlinks = new ArrayList<String>(
+              Preferences.getSequenceURLLinks());
       SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
@@ -331,14 +320,14 @@ public class IdPanel extends JPanel implements MouseListener,
           {
             for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
             {
-              nlinks.addElement(sf[sl].links.elementAt(l));
+              nlinks.add(sf[sl].links.elementAt(l));
             }
           }
         }
       }
 
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
-              nlinks, new Vector(Preferences.getGroupURLLinks()));
+      PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
+              Preferences.getGroupURLLinks());
       pop.show(this, e.getX(), e.getY());
 
       return;

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index fee47e5..8953487 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -33,7 +33,6 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -62,6 +61,7 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Hashtable;
@@ -215,19 +215,6 @@ public class PopupMenu extends JPopupMenu
   JMenuItem hideInsertions = new JMenuItem();
 
   /**
-   * Creates a new PopupMenu object.
-   * 
-   * @param ap
-   *          DOCUMENT ME!
-   * @param seq
-   *          DOCUMENT ME!
-   */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
-  {
-    this(ap, seq, links, null);
-  }
-
-  /**
    * 
    * @param ap
    * @param seq
@@ -235,7 +222,7 @@ public class PopupMenu extends JPopupMenu
    * @param groupLinks
    */
   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
-          Vector links, Vector groupLinks)
+          List<String> links, List<String> groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -616,10 +603,10 @@ public class PopupMenu extends JPopupMenu
     {
 
       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-      Vector linkset = new Vector();
+      List<String> linkset = new ArrayList<String>();
       for (int i = 0; i < links.size(); i++)
       {
-        String link = links.elementAt(i).toString();
+        String link = links.get(i);
         UrlLink urlLink = null;
         try
         {
@@ -670,7 +657,7 @@ public class PopupMenu extends JPopupMenu
                 {
                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                   {
-                    linkset.addElement(urls[u] + "|" + urls[u + 1]);
+                    linkset.add(urls[u] + "|" + urls[u + 1]);
                     addshowLink(linkMenu, label + "|" + urls[u],
                             urls[u + 1]);
                   }
@@ -688,7 +675,7 @@ public class PopupMenu extends JPopupMenu
               {
                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                 {
-                  linkset.addElement(urls[u] + "|" + urls[u + 1]);
+                  linkset.add(urls[u] + "|" + urls[u + 1]);
                   addshowLink(linkMenu, label, urls[u + 1]);
                 }
               }
@@ -706,7 +693,7 @@ public class PopupMenu extends JPopupMenu
               {
                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                 {
-                  linkset.addElement(urls[u] + "|" + urls[u + 1]);
+                  linkset.add(urls[u] + "|" + urls[u + 1]);
                   addshowLink(linkMenu, label, urls[u + 1]);
                 }
               }
@@ -717,7 +704,7 @@ public class PopupMenu extends JPopupMenu
         {
           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
           {
-            linkset.addElement(label + "|" + urlLink.getUrl_prefix());
+            linkset.add(label + "|" + urlLink.getUrl_prefix());
             // Add a non-dynamic link
             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
           }
@@ -861,7 +848,7 @@ public class PopupMenu extends JPopupMenu
     showOrHideMenu.add(item);
   }
 
-  private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
+  private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
   {
 
     // TODO: usability: thread off the generation of group url content so root
@@ -929,7 +916,7 @@ public class PopupMenu extends JPopupMenu
                              // to user
     for (int i = 0; i < groupLinks.size(); i++)
     {
-      String link = groupLinks.elementAt(i).toString();
+      String link = groupLinks.get(i);
       GroupUrlLink urlLink = null;
       try
       {

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 5cb6512..33ed0ae 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -29,7 +29,9 @@ import jalview.io.JalviewFileView;
 import jalview.jbgui.GPreferences;
 import jalview.jbgui.GSequenceLink;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -39,10 +41,9 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.io.File;
-import java.util.Collection;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
 import javax.help.HelpSetException;
 import javax.swing.JColorChooser;
@@ -95,7 +96,7 @@ public class Preferences extends GPreferences
    * Holds name and link separated with | character. Sequence ID must be
    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
    */
-  public static Vector sequenceURLLinks;
+  private static List<String> sequenceURLLinks;
 
   /**
    * Holds name and link separated with | character. Sequence IDS and Sequences
@@ -105,14 +106,25 @@ public class Preferences extends GPreferences
    * (TODO: proper escape for using | to separate ids or sequences
    */
 
-  public static Vector groupURLLinks;
+  private static List<String> groupURLLinks;
+
+  List<String> nameLinks;
+
+  List<String> urlLinks;
+
+  JInternalFrame frame;
+
+  DasSourceBrowser dasSource;
+
+  private WsPreferences wsPrefs;
+
   static
   {
     String string = Cache
             .getDefault(
                     "SEQUENCE_LINKS",
                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
-    sequenceURLLinks = new Vector();
+    sequenceURLLinks = new ArrayList<String>();
 
     try
     {
@@ -127,7 +139,7 @@ public class Preferences extends GPreferences
         {
           url = url + "|" + st.nextToken();
         }
-        sequenceURLLinks.addElement(name + "|" + url);
+        sequenceURLLinks.add(name + "|" + url);
       }
     } catch (Exception ex)
     {
@@ -140,9 +152,8 @@ public class Preferences extends GPreferences
       if (srsPos > -1)
       {
         sequenceURLLinks
-                .setElementAt(
-                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                        srsPos);
+                .set(srsPos,
+                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
       }
     }
 
@@ -151,17 +162,9 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new Vector();
+    groupURLLinks = new ArrayList<String>();
   }
 
-  Vector nameLinks, urlLinks;
-
-  JInternalFrame frame;
-
-  DasSourceBrowser dasSource;
-
-  private WsPreferences wsPrefs;
-
   /**
    * Creates a new Preferences object.
    */
@@ -175,7 +178,7 @@ public class Preferences extends GPreferences
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
     int width = 500, height = 450;
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
       width = 570;
       height = 480;
@@ -316,13 +319,13 @@ public class Preferences extends GPreferences
     /*
      * Set Connections tab defaults
      */
-    nameLinks = new Vector();
-    urlLinks = new Vector();
+    nameLinks = new ArrayList<String>();
+    urlLinks = new ArrayList<String>();
     for (int i = 0; i < sequenceURLLinks.size(); i++)
     {
-      String link = sequenceURLLinks.elementAt(i).toString();
-      nameLinks.addElement(link.substring(0, link.indexOf("|")));
-      urlLinks.addElement(link.substring(link.indexOf("|") + 1));
+      String link = sequenceURLLinks.get(i).toString();
+      nameLinks.add(link.substring(0, link.indexOf("|")));
+      urlLinks.add(link.substring(link.indexOf("|") + 1));
     }
 
     updateLinkData();
@@ -511,17 +514,17 @@ public class Preferences extends GPreferences
      */
     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 
-    jalview.util.BrowserLauncher.resetBrowser();
+    BrowserLauncher.resetBrowser();
 
     if (nameLinks.size() > 0)
     {
       StringBuffer links = new StringBuffer();
-      sequenceURLLinks = new Vector();
+      sequenceURLLinks = new ArrayList<String>();
       for (int i = 0; i < nameLinks.size(); i++)
       {
-        sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
-                + urlLinks.elementAt(i));
-        links.append(sequenceURLLinks.elementAt(i).toString());
+        sequenceURLLinks.add(nameLinks.get(i) + "|"
+                + urlLinks.get(i));
+        links.append(sequenceURLLinks.get(i).toString());
         links.append("|");
       }
       // remove last "|"
@@ -579,6 +582,8 @@ public class Preferences extends GPreferences
             Boolean.toString(clustaljv.isSelected()));
     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
             Boolean.toString(fastajv.isSelected()));
+    Cache.applicationProperties.setProperty("MEGA_JVSUFFIX",
+            Boolean.toString(megajv.isSelected()));
     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
             Boolean.toString(msfjv.isSelected()));
     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
@@ -651,9 +656,9 @@ public class Preferences extends GPreferences
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
-                "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-                "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
-                "PIR", "BLC", "Jalview" },
+                "fa, fasta, fastq", "aln", "pfam", "meg", "msf", "pir",
+                "blc", "jar" }, new String[] { "Fasta", "Clustal", "PFAM",
+                "MEGA", "MSF", "PIR", "BLC", "Jalview" },
             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
@@ -720,8 +725,8 @@ public class Preferences extends GPreferences
       {
         if (link.checkValid())
         {
-          nameLinks.addElement(link.getName());
-          urlLinks.addElement(link.getURL());
+          nameLinks.add(link.getName());
+          urlLinks.add(link.getURL());
           updateLinkData();
           valid = true;
         }
@@ -747,8 +752,8 @@ public class Preferences extends GPreferences
       return;
     }
 
-    link.setName(nameLinks.elementAt(index).toString());
-    link.setURL(urlLinks.elementAt(index).toString());
+    link.setName(nameLinks.get(index).toString());
+    link.setURL(urlLinks.get(index).toString());
 
     boolean valid = false;
     while (!valid)
@@ -760,8 +765,8 @@ public class Preferences extends GPreferences
       {
         if (link.checkValid())
         {
-          nameLinks.setElementAt(link.getName(), index);
-          urlLinks.setElementAt(link.getURL(), index);
+          nameLinks.set(index, link.getName());
+          urlLinks.set(index, link.getURL());
           updateLinkData();
           valid = true;
         }
@@ -785,15 +790,15 @@ public class Preferences extends GPreferences
               JOptionPane.WARNING_MESSAGE);
       return;
     }
-    nameLinks.removeElementAt(index);
-    urlLinks.removeElementAt(index);
+    nameLinks.remove(index);
+    urlLinks.remove(index);
     updateLinkData();
   }
 
   void updateLinkData()
   {
-    linkNameList.setListData(nameLinks);
-    linkURLList.setListData(urlLinks);
+    linkNameList.setListData(nameLinks.toArray(new String[nameLinks.size()]));
+    linkURLList.setListData(urlLinks.toArray(new String[urlLinks.size()]));
   }
 
   public void defaultBrowser_mouseClicked(MouseEvent e)
@@ -811,22 +816,14 @@ public class Preferences extends GPreferences
 
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see
-   * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
-   * .ActionEvent)
-   */
-  protected void showunconserved_actionPerformed(ActionEvent e)
+  public static List<String> getGroupURLLinks()
   {
-    // TODO Auto-generated method stub
-    super.showunconserved_actionPerformed(e);
+    return groupURLLinks;
   }
 
-  public static Collection getGroupURLLinks()
+  public static List<String> getSequenceURLLinks()
   {
-    return groupURLLinks;
+    return sequenceURLLinks;
   }
 
   @Override

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4ee87fc..30d7d63 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -54,8 +54,8 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
@@ -1601,19 +1601,19 @@ public class SeqPanel extends JPanel implements MouseListener,
       List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
               .findFeaturesAtRes(sequence.getDatasetSequence(),
                       sequence.findPosition(res));
-      Vector links = new Vector();
+      List<String> links = new ArrayList<String>();
       for (SequenceFeature sf : allFeatures)
       {
         if (sf.links != null)
         {
           for (int j = 0; j < sf.links.size(); j++)
           {
-            links.addElement(sf.links.elementAt(j));
+            links.add(sf.links.elementAt(j));
           }
         }
       }
 
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+      PopupMenu pop = new PopupMenu(ap, null, links, null);
       pop.show(this, evt.getX(), evt.getY());
       return;
     }

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index b12355a..40c5173 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -170,7 +170,7 @@ public class GPreferences extends JPanel
   /*
    * Connections tab components
    */
-  protected JList linkURLList = new JList();
+  protected JList<String> linkURLList = new JList<String>();
 
   protected JTextField proxyServerTB = new JTextField();
 
@@ -178,7 +178,7 @@ public class GPreferences extends JPanel
 
   protected JTextField defaultBrowser = new JTextField();
 
-  protected JList linkNameList = new JList();
+  protected JList<String> linkNameList = new JList<String>();
 
   protected JCheckBox useProxy = new JCheckBox();
 
@@ -205,6 +205,8 @@ public class GPreferences extends JPanel
 
   protected JCheckBox clustaljv = new JCheckBox();
 
+  protected JCheckBox megajv = new JCheckBox();
+
   protected JCheckBox msfjv = new JCheckBox();
 
   protected JCheckBox fastajv = new JCheckBox();

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index edf3202..400a9cb 100644 (file)
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -69,7 +69,7 @@ public class PopupMenuTest
             AppletFormatAdapter.PASTE, "FASTA");
     AlignFrame af = new AlignFrame(alignment, 700, 500);
     parentPanel = new AlignmentPanel(af, af.getViewport());
-    testee = new PopupMenu(parentPanel, null, null);
+    testee = new PopupMenu(parentPanel, null, null, null);
     int i = 0;
     for (SequenceI seq : alignment.getSequences())
     {