X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=36a06546a19cb64be81e905c321c8724eaf38d54;hb=60882e03a690898a0fb09053c28c5adb6eb6ea8d;hp=eb744544ea74f33a4f33f8ed75037db17453a67f;hpb=22b9e04a8351aef1cb23a66d898502601499b673;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index eb74454..36a0654 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -41,6 +41,8 @@ public class FeatureSettings extends JPanel
   JTable table;
   JPanel groupPanel;
 
+  boolean alignmentHasFeatures = false;
+
   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
   {
     this.ap = ap;
@@ -50,6 +52,7 @@ public class FeatureSettings extends JPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
     setTableData();
 
@@ -124,8 +127,13 @@ public class FeatureSettings extends JPanel
     bigPanel.add(transPanel, BorderLayout.SOUTH);
     bigPanel.add(scrollPane, BorderLayout.CENTER);
     if(groupPanel!=null)
-      bigPanel.add(groupPanel, BorderLayout.NORTH);
+    {
+      groupPanel.setLayout(
+          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
 
+      groupPanel.validate();
+      bigPanel.add(groupPanel, BorderLayout.NORTH);
+    }
     add(bigPanel, BorderLayout.CENTER);
     add(buttonPanel, BorderLayout.SOUTH);
 
@@ -134,60 +142,78 @@ public class FeatureSettings extends JPanel
 
   void setTableData()
   {
+    alignmentHasFeatures = false;
+
     if (fr.featureGroups == null)
       fr.featureGroups = new Hashtable();
-    else
-      fr.featureGroups.clear();
 
     Vector allFeatures = new Vector();
-    Vector features;
-    Enumeration e;
-    SequenceFeature sf;
-
-  for (int i = 0; i < av.alignment.getHeight(); i++)
-  {
-    features = av.alignment.getSequenceAt(i).getDatasetSequence().
-        getSequenceFeatures();
-    if (features == null)
-      continue;
+    Vector allGroups = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group;
 
-    e = features.elements();
-    while (e.hasMoreElements())
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      sf = (SequenceFeature) e.nextElement();
-      if(sf.getFeatureGroup()!=null
-          && !fr.featureGroups.containsKey(sf.getFeatureGroup()))
+      if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
+        continue;
+
+      alignmentHasFeatures = true;
+
+      tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        if(tmpfeatures[index].getFeatureGroup()!=null)
+        {
+          group = tmpfeatures[index].featureGroup;
+          if(!allGroups.contains(group))
+           {
+             allGroups.addElement(group);
+
+             boolean visible = true;
+             if (fr.featureGroups.containsKey(group))
+             {
+               visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+             }
+
+             fr.featureGroups.put(group, new Boolean(visible));
+
+             if (groupPanel == null)
+             {
+               groupPanel = new JPanel();
+             }
+
+             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()));
+                 ap.seqPanel.seqCanvas.repaint();
+                 if (ap.overviewPanel != null)
+                   ap.overviewPanel.updateOverviewImage();
+
+                 resetTable(true);
+               }
+             });
+             groupPanel.add(check);
+
+           }
+
+       }
+
+       if (!allFeatures.contains(tmpfeatures[index].getType()))
        {
-         fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));
-         if(groupPanel==null)
-            groupPanel = new JPanel();
-
-          final JCheckBox check = new JCheckBox(sf.getFeatureGroup(), true);
-          check.setFont(new Font("Serif", Font.BOLD, 12));
-          check.addItemListener(new ItemListener()
-              {
-                public void itemStateChanged(ItemEvent evt)
-                {
-                  if (fr.featureGroups.containsKey(check.getText()))
-                  {
-                    fr.featureGroups.put(check.getText(),
-                                         new Boolean(check.isSelected()));
-                    ap.seqPanel.seqCanvas.repaint();
-                    if (ap.overviewPanel != null)
-                      ap.overviewPanel.updateOverviewImage();
-                  }
-
-                }
-              });
-          groupPanel.add(check);
+           allFeatures.addElement(tmpfeatures[index].getType());
        }
-      if (!allFeatures.contains(sf.getType()))
-      {
-        allFeatures.addElement(sf.getType());
-      }
+       index ++;
     }
   }
-    if(allFeatures.size()<1)
+
+
+    if(!alignmentHasFeatures)
      {
        try
        { frame.setClosed(true);  }
@@ -200,88 +226,133 @@ public class FeatureSettings extends JPanel
        return;
      }
 
-    int fSize = allFeatures.size();
+     resetTable(false);
+  }
+
+  void resetTable(boolean groupsChanged)
+  {
+   SequenceFeature [] tmpfeatures;
+   String group=null, type;
+   Vector visibleChecks = new Vector();
+
+   //Find out which features should be visible depending on which groups
+   //are selected / deselected
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+        if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
+          continue;
 
-    String type;
-    boolean originalExists = false;
-    if(originalData!=null)
-      originalExists = true;
-    else
-      originalData = new Object[fSize][3];
+        tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+        int index = 0;
+        while (index < tmpfeatures.length)
+        {
+          group = tmpfeatures[index].featureGroup;
 
+          if (group==null || fr.featureGroups.get(group)==null ||
+              ((Boolean) fr.featureGroups.get(group)).booleanValue())
+          {
+            type = tmpfeatures[index].getType();
+            if(!visibleChecks.contains(type) )
+            {
+              visibleChecks.addElement(type);
+            }
+          }
+          index++;
+        }
+    }
+
+    int fSize = visibleChecks.size();
     Object [][] data = new Object[fSize][3];
-    for(int i=0; i<fSize; i++)
+    int dataIndex = 0;
+
+    if(fr.renderOrder!=null)
     {
-      type = allFeatures.elementAt(i).toString();
-      Color col = fr.getColour(type);
-      data[i][0]=type;
-      data[i][1]=col;
-      if(fr.featuresDisplayed!=null)
-         data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
-      else
-        data[i][2] = new Boolean(true);
-
-      if(!originalExists)
+      //First add the checks in the previous render order,
+      //in case the window has been closed and reopened
+      for(int ro=fr.renderOrder.length-1; ro>-1; ro--)
       {
-        originalData[i][0] = type;
-        originalData[i][1] = col;
-        if (fr.featuresDisplayed != null)
-          originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
-        else
-          originalData[i][2] = new Boolean(true);
+           type = fr.renderOrder[ro];
+
+           if(!visibleChecks.contains(type))
+             continue;
+
+           data[dataIndex][0] = type;
+           data[dataIndex][1] = fr.getColour(type);
+           data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
+           dataIndex++;
+           visibleChecks.removeElement(type);
       }
     }
-    ////////////////////////////////////
-        //Now build the table
-        table = new JTable(new FeatureTableModel(data));
-        scrollPane.setViewportView(table);
-        table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
-        table.setFont(new Font("Verdana", Font.PLAIN, 12));
-        table.setDefaultRenderer(Color.class,
-                             new ColorRenderer());
 
-        table.setDefaultEditor(Color.class,
-                          new ColorEditor());
+    fSize = visibleChecks.size();
+    for(int i=0; i<fSize; i++)
+    {
+      //These must be extra features belonging to the group
+      //which was just selected
+      type = visibleChecks.elementAt(i).toString();
+      data[dataIndex][0] = type;
+      data[dataIndex][1] = fr.getColour(type);
+      data[dataIndex][2] = new Boolean(true);
+      dataIndex++;
+    }
+
+    if(originalData==null)
+    {
+      originalData = new Object[data.length][3];
+      System.arraycopy(data,0,originalData,0,data.length);
+    }
+
+    table = new JTable(new FeatureTableModel(data));
+    scrollPane.setViewportView(table);
+    table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+    table.setFont(new Font("Verdana", Font.PLAIN, 12));
+    table.setDefaultRenderer(Color.class,
+                         new ColorRenderer());
 
-        table.getColumnModel().getColumn(0).setPreferredWidth(200);
+    table.setDefaultEditor(Color.class,
+                      new ColorEditor());
 
-        table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    table.getColumnModel().getColumn(0).setPreferredWidth(200);
 
-        table.addMouseListener(new MouseAdapter()
-            {
-              public void mousePressed(MouseEvent evt)
-              {
-                selectedRow = table.rowAtPoint(evt.getPoint());
-              }
-            });
+    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
-        table.addMouseMotionListener(new MouseMotionAdapter()
-            {
-              public void mouseDragged(MouseEvent evt)
-              {
-                int newRow = table.rowAtPoint(evt.getPoint());
-                if(newRow!=selectedRow
-                   && selectedRow!=-1
-                   && newRow!=-1)
-                {
-                  Object[] temp = new Object[3];
-                  temp[0] = table.getValueAt(selectedRow, 0);
-                  temp[1] = table.getValueAt(selectedRow, 1);
-                  temp[2] = table.getValueAt(selectedRow, 2);
-
-                  table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-                  table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-                  table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
-
-                  table.setValueAt(temp[0], newRow, 0);
-                  table.setValueAt(temp[1], newRow, 1);
-                  table.setValueAt(temp[2], newRow, 2);
-
-                  selectedRow = newRow;
-                }
-              }
+    table.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            selectedRow = table.rowAtPoint(evt.getPoint());
+          }
         });
 
+    table.addMouseMotionListener(new MouseMotionAdapter()
+        {
+          public void mouseDragged(MouseEvent evt)
+          {
+            int newRow = table.rowAtPoint(evt.getPoint());
+            if(newRow!=selectedRow
+               && selectedRow!=-1
+               && newRow!=-1)
+            {
+              Object[] temp = new Object[3];
+              temp[0] = table.getValueAt(selectedRow, 0);
+              temp[1] = table.getValueAt(selectedRow, 1);
+              temp[2] = table.getValueAt(selectedRow, 2);
+
+              table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
+              table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
+              table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
+
+              table.setValueAt(temp[0], newRow, 0);
+              table.setValueAt(temp[1], newRow, 1);
+              table.setValueAt(temp[2], newRow, 2);
+
+              selectedRow = newRow;
+            }
+          }
+    });
+
+    updateFeatureRenderer(data);
+
   }
 
   void load()
@@ -400,6 +471,11 @@ public class FeatureSettings extends JPanel
             return data;
           }
 
+          public void setData(Object[][] data)
+          {
+            this.data = data;
+          }
+
           public int getColumnCount() {
               return columnNames.length;
           }