X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=ea492e245bc134a1ca76a15210afe2b3d389ec80;hb=50ea78c7b98de7614cd386956e9aa0ee73dd7936;hp=6c5990a80aff82a1adec14bc38264c7c8fbfd115;hpb=2bc54fc3fc79e09819a6e650ecd38446322a5f3c;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6c5990a..ea492e2 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -37,7 +37,7 @@ public class FeatureSettings
     extends JPanel
 {
   DasSourceBrowser dassourceBrowser;
-  jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
+  jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
   JPanel settingsPane = new JPanel();
   JPanel dasSettingsPane = new JPanel();
 
@@ -132,13 +132,13 @@ public class FeatureSettings
       {
         if (!fs.resettingTable && !fs.handlingUpdate) {
           fs.handlingUpdate=true;
-          fs.resetTable(new String[] {}); // groups may be added
+          fs.resetTable(null); // new groups may be added with new seuqence feature types only
           fs.handlingUpdate=false;
         }
       }
-      
+
     });
-    
+
     frame = new JInternalFrame();
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
@@ -157,7 +157,7 @@ public class FeatureSettings
    * true when Feature Settings are updating from feature renderer
    */
   private boolean handlingUpdate=false;
-  
+
   /**
    * contains a float[3] for each feature type string. created by setTableData
    */
@@ -198,57 +198,10 @@ public class FeatureSettings
           if (!allGroups.contains(group))
           {
             allGroups.addElement(group);
-
-            boolean visible;
-            if (fr.featureGroups.containsKey(group))
+            if (group!=null)
             {
-              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
-            } else {
-              visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType());
+              checkGroupState(group);
             }
-
-            if (groupPanel == null)
-            {
-              groupPanel = new JPanel();
-            }
-
-            boolean alreadyAdded = false;
-            for (int g = 0; g < groupPanel.getComponentCount(); g++)
-            {
-              if ( ( (JCheckBox) groupPanel.getComponent(g))
-                  .getText().equals(group))
-              {
-                alreadyAdded = true;
-                break;
-              }
-            }
-
-            if (alreadyAdded)
-            {
-              
-              continue;
-            }
-
-            fr.featureGroups.put(group, new Boolean(visible));
-            final String grp = group;
-            final JCheckBox check = new JCheckBox(group, visible);
-            check.setFont(new Font("Serif", Font.BOLD, 12));
-            check.addItemListener(new ItemListener()
-            {
-              public void itemStateChanged(ItemEvent evt)
-              {
-                fr.featureGroups.put(check.getText(),
-                                     new Boolean(check.isSelected()));
-                af.alignPanel.seqPanel.seqCanvas.repaint();
-                if (af.alignPanel.overviewPanel != null)
-                {
-                  af.alignPanel.overviewPanel.updateOverviewImage();
-                }
-
-                resetTable(new String[] { grp } );
-              }
-            });
-            groupPanel.add(check);
           }
         }
 
@@ -259,17 +212,79 @@ public class FeatureSettings
         index++;
       }
     }
-    
+
     resetTable(null);
 
     validate();
   }
+  /**
+   *
+   * @param group
+   * @return true if group has been seen before and is already added to set.
+   */
+  private boolean checkGroupState(String group) {
+    boolean visible;
+    if (fr.featureGroups.containsKey(group))
+    {
+      visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+        } else {
+        visible=true; // new group is always made visible
+      }
+
+      if (groupPanel == null)
+      {
+        groupPanel = new JPanel();
+      }
+
+      boolean alreadyAdded = false;
+      for (int g = 0; g < groupPanel.getComponentCount(); g++)
+      {
+        if ( ( (JCheckBox) groupPanel.getComponent(g))
+            .getText().equals(group))
+        {
+          alreadyAdded = true;
+          ((JCheckBox)groupPanel.getComponent(g)).setSelected(visible);
+          break;
+        }
+      }
+
+      if (alreadyAdded)
+      {
+
+        return true;
+      }
+
+      fr.featureGroups.put(group, new Boolean(visible));
+      final String grp = group;
+      final JCheckBox check = new JCheckBox(group, visible);
+      check.setFont(new Font("Serif", Font.BOLD, 12));
+      check.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent evt)
+        {
+          fr.featureGroups.put(check.getText(),
+                               new Boolean(check.isSelected()));
+          af.alignPanel.seqPanel.seqCanvas.repaint();
+          if (af.alignPanel.overviewPanel != null)
+          {
+            af.alignPanel.overviewPanel.updateOverviewImage();
+          }
+
+          resetTable(new String[] { grp } );
+        }
+      });
+      groupPanel.add(check);
+      return false;
+  }
   boolean resettingTable=false;
-  void resetTable(String[] groupChanged)
+  synchronized void resetTable(String[] groupChanged)
   {
+    if (resettingTable==true)
+    {
+      return;
+    }
     resettingTable=true;
     typeWidth=new Hashtable();
-    Vector groupchanged = new Vector();
     // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
     float[] avWidth=null;
     SequenceFeature[] tmpfeatures;
@@ -303,6 +318,8 @@ public class FeatureSettings
         if (group == null || fr.featureGroups.get(group) == null ||
             ( (Boolean) fr.featureGroups.get(group)).booleanValue())
         {
+          if (group!=null)
+            checkGroupState(group);
           type = tmpfeatures[index].getType();
           if (!visibleChecks.contains(type))
           {
@@ -551,16 +568,16 @@ public class FeatureSettings
     boolean sort=false;
     for (int i=0;i<width.length; i++) {
       //awidth = (float[]) typeWidth.get(data[i][0]);
-      if (width[i]==0) 
+      if (width[i]==0)
       {
         width[i] = fr.getOrder(data[i][0].toString());
         if (width[i]<0)
         {
           width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
         }
-      } else { 
+      } else {
         width[i] /=max; // normalize
-        fr.setOrder(data[i][0].toString(), width[i]); // store for later 
+        fr.setOrder(data[i][0].toString(), width[i]); // store for later
       }
       if (i>0)
         sort = sort || width[i-1]>width[i];
@@ -568,7 +585,7 @@ public class FeatureSettings
     if (sort)
       jalview.util.QuickSort.sort(width, data);
     // update global priority order
-    
+
     updateFeatureRenderer(data,false);
     table.repaint();
   }
@@ -591,11 +608,6 @@ public class FeatureSettings
   {
     fr.setFeaturePriority(data, visibleNew);
     af.alignPanel.paintAlignment(true);
-
-    if (af.alignPanel.overviewPanel != null)
-    {
-      af.alignPanel.overviewPanel.updateOverviewImage();
-    }
   }
 
   int selectedRow = -1;
@@ -740,23 +752,32 @@ public class FeatureSettings
     fetchDAS.setEnabled(false);
     cancelDAS.setEnabled(true);
     Vector selectedSources = dassourceBrowser.getSelectedSources();
-
+    doDasFeatureFetch(selectedSources, true, true);
+  }
+  /**
+   * get the features from selectedSources for all or the current selection
+   * @param selectedSources
+   * @param checkDbRefs
+   * @param promptFetchDbRefs
+   */
+  private void doDasFeatureFetch(Vector selectedSources, boolean checkDbRefs, boolean promptFetchDbRefs)
+  {
     SequenceI[] dataset, seqs;
     int iSize;
-
-    if (af.getViewport().getSelectionGroup() != null
-        && af.getViewport().getSelectionGroup().getSize() > 0)
+    AlignViewport vp = af.getViewport();
+    if (vp.getSelectionGroup() != null
+        && vp.getSelectionGroup().getSize() > 0)
     {
-      iSize = af.getViewport().getSelectionGroup().getSize();
+      iSize = vp.getSelectionGroup().getSize();
       dataset = new SequenceI[iSize];
-      seqs = af.getViewport().getSelectionGroup().
+      seqs = vp.getSelectionGroup().
           getSequencesInOrder(
-              af.getViewport().getAlignment());
+              vp.getAlignment());
     }
     else
     {
-      iSize = af.getViewport().getAlignment().getHeight();
-      seqs = af.getViewport().getAlignment().getSequencesArray();
+      iSize = vp.getAlignment().getHeight();
+      seqs = vp.getAlignment().getSequencesArray();
     }
 
     dataset = new SequenceI[iSize];
@@ -765,15 +786,64 @@ public class FeatureSettings
       dataset[i] = seqs[i].getDatasetSequence();
     }
 
+    cancelDAS.setEnabled(true);
     dasFeatureFetcher =
-        new jalview.io.DasSequenceFeatureFetcher(
+        new jalview.ws.DasSequenceFeatureFetcher(
             dataset,
             this,
-            selectedSources);
-    cancelDAS.setEnabled(true);
+            selectedSources, checkDbRefs, promptFetchDbRefs);
     af.getViewport().setShowSequenceFeatures(true);
     af.showSeqFeatures.setSelected(true);
   }
+  /**
+   * properly initialise DAS fetcher and then initiate a new thread to fetch features from the named sources (rather than any turned on by default) 
+   * @param sources
+   */
+  public void fetchDasFeatures(Vector sources)
+  {
+    Thread thr = new Thread(new Runnable() {
+      public void run() {
+        // this actually initialises the das source list
+        dassourceBrowser.paintComponent(null); // yuk
+      }
+    });
+    thr.start();
+    while (dassourceBrowser.loadingDasSources || dassourceBrowser.dasSources==null)
+    {
+      try { Thread.sleep(10); } catch (Exception e) {};
+    }
+    Vector resolved = new Vector();
+    if (sources!=null)
+    {
+      for (int i=0;i<dassourceBrowser.dasSources.length; i++)
+      {
+        if (sources.contains(dassourceBrowser.dasSources[i].getNickname()))
+        {
+          if (!resolved.contains(dassourceBrowser.dasSources[i]))
+          {
+            resolved.addElement(dassourceBrowser.dasSources[i]);
+          }
+        }
+      }
+    }
+    if (resolved.size()==0)
+    {
+      resolved = dassourceBrowser.getSelectedSources();
+    }
+    if (resolved.size()>0)
+    {
+      final Vector dassources = resolved;
+      SwingUtilities.invokeLater(new Runnable() {
+
+        public void run()
+        {
+          fetchDAS.setEnabled(false);
+          cancelDAS.setEnabled(true);
+          doDasFeatureFetch(dassources, true, false);
+          
+        }});
+    }
+  }
 
   public void saveDAS_actionPerformed(ActionEvent e)
   {
@@ -788,10 +858,24 @@ public class FeatureSettings
 
   public void cancelDAS_actionPerformed(ActionEvent e)
   {
-    dasFeatureFetcher.cancel();
+    if (dasFeatureFetcher!=null)
+    {
+      dasFeatureFetcher.cancel();
+    }
     fetchDAS.setEnabled(true);
     cancelDAS.setEnabled(false);
   }
+  public void noDasSourceActive()
+  {
+    complete();
+    JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            "No das sources were selected.\n"
+            + "Please select some sources and\n"
+            +" try again.",
+            "No Sources Selected",
+            JOptionPane.DEFAULT_OPTION,
+            JOptionPane.INFORMATION_MESSAGE);
+  }
 
   /////////////////////////////////////////////////////////////////////////
   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html