X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=15e269c5a91b64c2269103088d6b8a8cf68b1060;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=f6e7d44ca6bdca5f56b7efa1ad754995628e3aca;hpb=81aaad88042de8ba97baf33da5185c04ab71aacc;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index f6e7d44..15e269c 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,345 +1,472 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class IdPanel
-    extends Panel implements MouseListener, MouseMotionListener
-{
-
-  protected IdCanvas idCanvas;
-  protected AlignViewport av;
-  protected AlignmentPanel alignPanel;
-  ScrollThread scrollThread = null;
-
-  int offy;
-  int width;
-  int lastid = -1;
-  boolean mouseDragging = false;
-  java.util.Vector links = new java.util.Vector();
-
-  public IdPanel(AlignViewport av, AlignmentPanel parent)
-  {
-    this.av = av;
-    alignPanel = parent;
-    idCanvas = new IdCanvas(av);
-    setLayout(new BorderLayout());
-    add(idCanvas, BorderLayout.CENTER);
-    idCanvas.addMouseListener(this);
-    idCanvas.addMouseMotionListener(this);
-
-    String label, url;
-    if(av.applet!=null)
-    {
-      for (int i = 1; i < 10; i++)
-      {
-        label = av.applet.getParameter("linkLabel_" + i);
-        url = av.applet.getParameter("linkURL_" + i);
-
-        if (label != null && url != null)
-          links.addElement(label + "|" + url);
-
-      }
-    }
-    if (links.size() < 1)
-    {
-      links = new java.util.Vector();
-      links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
-    }
-  }
-
-  Tooltip tooltip;
-  public void mouseMoved(MouseEvent e)
-  {
-    int seq = alignPanel.seqPanel.findSeq(e);
-
-    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
-    if(sequence.getDescription()==null)
-    {
-      if(tooltip!=null)
-        tooltip.setVisible(false);
-      tooltip = null;
-      return;
-    }
-
-    if (tooltip == null)
-      tooltip = new Tooltip(
-          sequence.getDisplayId(true)
-          + "\n" + sequence.getDescription(), idCanvas);
-    else
-      tooltip.setTip(sequence.getDisplayId(true)
-                     + "\n" + sequence.getDescription());
-
-    tooltip.repaint();
-
-  }
-
-  public void mouseDragged(MouseEvent e)
-  {
-    mouseDragging = true;
-
-    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
-
-    if (seq < lastid)
-    {
-      selectSeqs(lastid - 1, seq);
-    }
-    else if (seq > lastid)
-    {
-      selectSeqs(lastid + 1, seq);
-    }
-
-    lastid = seq;
-    alignPanel.repaint();
-  }
-
-  public void mouseClicked(MouseEvent e)
-  {
-    if (e.getClickCount() < 2)
-        return;
-
-
-    //DEFAULT LINK IS FIRST IN THE LINK LIST
-    int seq = alignPanel.seqPanel.findSeq(e);
-    String id = av.getAlignment().getSequenceAt(seq).getName();
-    if (id.indexOf("|") > -1)
-        id = id.substring(id.lastIndexOf("|") + 1);
-
-    String target = links.elementAt(0).toString();
-    target = target.substring(0, target.indexOf("|"));
-    String url = links.elementAt(0).toString();
-    url = url.substring(url.indexOf("|")+1);
-
-    int index = url.indexOf("$SEQUENCE_ID$");
-    url = url.substring(0, index)+ id + url.substring(index+13);
-
-    try
-    {
-
-      alignPanel.alignFrame.showURL(url, target);
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  public void mouseEntered(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-    }
-  }
-
-  public void mouseExited(MouseEvent e)
-  {
-    if (av.getWrapAlignment())
-    {
-      return;
-    }
-
-    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
-    {
-      scrollThread = new ScrollThread(true);
-    }
-
-    if (mouseDragging && e.getY() >= getSize().height &&
-        av.alignment.getHeight() > av.getEndSeq())
-    {
-      scrollThread = new ScrollThread(false);
-    }
-  }
-
-  public void mousePressed(MouseEvent e)
-  {
-    if (e.getClickCount() >1 )
-    {
-      return;
-    }
-
-    int y = e.getY();
-    if (av.getWrapAlignment())
-    {
-      y -= 2 * av.charHeight;
-    }
-
-    int seq = alignPanel.seqPanel.findSeq(e);
-
-    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
-        InputEvent.BUTTON3_MASK)
-    {
-      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);
-      this.add(popup);
-      popup.show(this, e.getX(), e.getY());
-      return;
-    }
-
-
-    if ((av.getSelectionGroup() == null) ||
-            ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
-    {
-      av.setSelectionGroup(new SequenceGroup());
-      av.getSelectionGroup().setStartRes(0);
-      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
-    }
-
-
-    if (e.isShiftDown() && lastid != -1)
-    {
-      selectSeqs(lastid, seq);
-    }
-    else
-    {
-      selectSeq(seq);
-    }
-
-    alignPanel.repaint();
-  }
-
-  void selectSeq(int seq)
-  {
-    lastid = seq;
-    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, false);
-  }
-
-  void selectSeqs(int start, int end)
-  {
-
-    lastid = start;
-
-    if (end >= av.getAlignment().getHeight())
-    {
-      end = av.getAlignment().getHeight() - 1;
-    }
-
-    if (end < start)
-    {
-      int tmp = start;
-      start = end;
-      end = tmp;
-      lastid = end;
-    }
-
-    for (int i = start; i <= end; i++)
-    {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
-    }
-
-  }
-
-  public void mouseReleased(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-    }
-
-    if(av.getSelectionGroup()!=null)
-      av.getSelectionGroup().recalcConservation();
-
-    mouseDragging = false;
-    PaintRefresher.Refresh(this, av.alignment);
-  }
-
-  public void highlightSearchResults(java.util.Vector found)
-  {
-    idCanvas.setHighlighted(found);
-
-    if (found == null)
-    {
-      return;
-    }
-
-    int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
-
-    // do we need to scroll the panel?
-    if (av.getStartSeq() > index || av.getEndSeq() < index)
-    {
-      alignPanel.setScrollValues(av.getStartRes(), index);
-    }
-  }
-
-  // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
-  {
-    boolean running = false;
-    boolean up = true;
-    public ScrollThread(boolean up)
-    {
-      this.up = up;
-      start();
-    }
-
-    public void stopScrolling()
-    {
-      running = false;
-    }
-
-    public void run()
-    {
-      running = true;
-      while (running)
-      {
-        if (alignPanel.scrollUp(up))
-        {
-          // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
-          if (!up)
-          {
-            seq = av.getEndSeq();
-          }
-
-          if (seq < lastid)
-          {
-            selectSeqs(lastid - 1, seq);
-          }
-          else if (seq > lastid && seq<av.alignment.getHeight())
-          {
-            selectSeqs(lastid + 1, seq);
-          }
-
-
-          lastid = seq;
-        }
-        else
-        {
-          running = false;
-        }
-
-        alignPanel.repaint();
-        try
-        {
-          Thread.sleep(100);
-        }
-        catch (Exception ex)
-        {}
-      }
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+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
+{
+
+  protected IdCanvas idCanvas;
+
+  protected AlignmentViewport av;
+
+  protected AlignmentPanel alignPanel;
+
+  ScrollThread scrollThread = null;
+
+  int lastid = -1;
+
+  boolean mouseDragging = false;
+
+  UrlProviderI urlProvider = null;
+
+  public IdPanel(AlignViewport viewport, AlignmentPanel parent)
+  {
+    this.av = viewport;
+    alignPanel = parent;
+    idCanvas = new IdCanvas(viewport);
+    setLayout(new BorderLayout());
+    add(idCanvas, BorderLayout.CENTER);
+    idCanvas.addMouseListener(this);
+    idCanvas.addMouseMotionListener(this);
+
+    String label, url;
+    // TODO: add in group link parameter
+
+    // make a list of label,url pairs
+    HashMap<String, String> urlList = new HashMap<>();
+    if (viewport.applet != null)
+    {
+      for (int i = 1; i < 10; i++)
+      {
+        label = viewport.applet.getParameter("linkLabel_" + i);
+        url = viewport.applet.getParameter("linkURL_" + i);
+
+        // only add non-null parameters
+        if (label != null)
+        {
+          urlList.put(label, url);
+        }
+      }
+
+      if (!urlList.isEmpty())
+      {
+        // set default as first entry in list
+        String defaultUrl = viewport.applet.getParameter("linkLabel_1");
+        UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+                defaultUrl, urlList);
+        urlProvider = factory.createUrlProvider();
+      }
+    }
+  }
+
+  Tooltip tooltip;
+
+  @Override
+  public void mouseMoved(MouseEvent e)
+  {
+    int seq = alignPanel.seqPanel.findSeq(e);
+
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+    StringBuffer tooltiptext = new StringBuffer();
+    if (sequence == 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(sf.getFeatureGroup());
+        nl = true;
+      }
+      if (sf.getType() != null)
+      {
+        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
+      if (tooltip != null)
+      {
+        tooltip.setVisible(false);
+      }
+      tooltip = null;
+      tooltiptext = null;
+      return;
+    }
+    if (tooltip == null)
+    {
+      tooltip = new Tooltip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+              idCanvas);
+    }
+    else
+    {
+      tooltip.setTip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
+    }
+    tooltiptext = null;
+  }
+
+  @Override
+  public void mouseDragged(MouseEvent e)
+  {
+    mouseDragging = true;
+
+    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+
+    if (seq < lastid)
+    {
+      selectSeqs(lastid - 1, seq);
+    }
+    else if (seq > lastid)
+    {
+      selectSeqs(lastid + 1, seq);
+    }
+
+    lastid = seq;
+    alignPanel.paintAlignment(false, false);
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent e)
+  {
+    if (e.getClickCount() < 2)
+    {
+      return;
+    }
+
+    // get the sequence details
+    int seq = alignPanel.seqPanel.findSeq(e);
+    SequenceI sq = av.getAlignment().getSequenceAt(seq);
+    if (sq == null)
+    {
+      return;
+    }
+    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
+    {
+      alignPanel.alignFrame.showURL(url, target);
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  @Override
+  public void mouseEntered(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+  }
+
+  @Override
+  public void mouseExited(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+    {
+      return;
+    }
+
+    if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
+    {
+      scrollThread = new ScrollThread(true);
+    }
+
+    if (mouseDragging && e.getY() >= getSize().height
+            && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
+    {
+      scrollThread = new ScrollThread(false);
+    }
+  }
+
+  @Override
+  public void mousePressed(MouseEvent e)
+  {
+    if (e.getClickCount() > 1)
+    {
+      return;
+    }
+
+    int y = e.getY();
+    if (av.getWrapAlignment())
+    {
+      y -= 2 * av.getCharHeight();
+    }
+
+    int seq = alignPanel.seqPanel.findSeq(e);
+
+    if ((e.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    {
+      SequenceI sq = av.getAlignment().getSequenceAt(seq);
+
+      /*
+       *  build a new links menu based on the current links
+       *  and any non-positional features
+       */
+      List<String> nlinks;
+      if (urlProvider != null)
+      {
+        nlinks = urlProvider.getLinksForMenu();
+      }
+      else
+      {
+        nlinks = new ArrayList<>();
+      }
+
+      for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
+      {
+        if (sf.links != null)
+        {
+          for (String link : sf.links)
+          {
+            nlinks.add(link);
+          }
+        }
+      }
+
+      APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
+      this.add(popup);
+      popup.show(this, e.getX(), e.getY());
+      return;
+    }
+
+    if ((av.getSelectionGroup() == null)
+            || ((!jalview.util.Platform.isControlDown(e)
+                    && !e.isShiftDown()) && av.getSelectionGroup() != null))
+    {
+      av.setSelectionGroup(new SequenceGroup());
+      av.getSelectionGroup().setStartRes(0);
+      av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
+    }
+
+    if (e.isShiftDown() && lastid != -1)
+    {
+      selectSeqs(lastid, seq);
+    }
+    else
+    {
+      selectSeq(seq);
+    }
+
+    alignPanel.paintAlignment(false, false);
+  }
+
+  void selectSeq(int seq)
+  {
+    lastid = seq;
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+  }
+
+  void selectSeqs(int start, int end)
+  {
+
+    lastid = start;
+
+    if (end >= av.getAlignment().getHeight())
+    {
+      end = av.getAlignment().getHeight() - 1;
+    }
+
+    if (end < start)
+    {
+      int tmp = start;
+      start = end;
+      end = tmp;
+      lastid = end;
+    }
+    if (av.getSelectionGroup() == null)
+    {
+      av.setSelectionGroup(new SequenceGroup());
+    }
+    for (int i = start; i <= end; i++)
+    {
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
+    }
+
+  }
+
+  @Override
+  public void mouseReleased(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+
+    if (av.getSelectionGroup() != null)
+    {
+      av.getSelectionGroup().recalcConservation();
+    }
+
+    mouseDragging = false;
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    // always send selection message when mouse is released
+    av.sendSelection();
+  }
+
+  public void highlightSearchResults(List<SequenceI> list)
+  {
+    idCanvas.setHighlighted(list);
+
+    if (list == null)
+    {
+      return;
+    }
+
+    int index = av.getAlignment().findIndex(list.get(0));
+
+    // do we need to scroll the panel?
+    if (av.getRanges().getStartSeq() > index
+            || av.getRanges().getEndSeq() < index)
+    {
+      av.getRanges().setStartSeq(index);
+    }
+  }
+
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread extends Thread
+  {
+    boolean running = false;
+
+    boolean up = true;
+
+    public ScrollThread(boolean isUp)
+    {
+      this.up = isUp;
+      start();
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    @Override
+    public void run()
+    {
+      running = true;
+      while (running)
+      {
+        if (av.getRanges().scrollUp(up))
+        {
+          // scroll was ok, so add new sequence to selection
+          int seq = av.getRanges().getStartSeq();
+          if (!up)
+          {
+            seq = av.getRanges().getEndSeq();
+          }
+
+          if (seq < lastid)
+          {
+            selectSeqs(lastid - 1, seq);
+          }
+          else if (seq > lastid && seq < av.getAlignment().getHeight())
+          {
+            selectSeqs(lastid + 1, seq);
+          }
+
+          lastid = seq;
+        }
+        else
+        {
+          running = false;
+        }
+
+        alignPanel.paintAlignment(true, false);
+        try
+        {
+          Thread.sleep(100);
+        } catch (Exception ex)
+        {
+        }
+      }
+    }
+  }
+}