X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=f14ec5141198ad29314a749ae00f5d27fe264838;hb=e02486484d33e20dedb020a34f31f6024d5720a2;hp=7c95ed78e19dd96e5aa029bfcd0292b057dcd16d;hpb=c0bf7be8f74d296a751836ee33bc328e2ff6d1b5;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 7c95ed7..f14ec51 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -35,13 +35,14 @@ public class FeatureSettings extends JPanel
   final FeatureRenderer fr;
   final AlignmentPanel ap;
   final AlignViewport av;
-  Hashtable allFeatures;
   Object [][] originalData;
   final JInternalFrame frame;
   JScrollPane scrollPane = new JScrollPane();
   JTable table;
   JPanel groupPanel;
 
+  boolean alignmentHasFeatures = false;
+
   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
   {
     this.ap = ap;
@@ -127,7 +128,8 @@ public class FeatureSettings extends JPanel
     if(groupPanel!=null)
     {
       groupPanel.setLayout(
-          new GridLayout(groupPanel.getComponentCount()/3, 4));
+          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+
       groupPanel.validate();
       bigPanel.add(groupPanel, BorderLayout.NORTH);
     }
@@ -139,62 +141,78 @@ public class FeatureSettings extends JPanel
 
   void setTableData()
   {
+    alignmentHasFeatures = false;
+
     if (fr.featureGroups == null)
       fr.featureGroups = new Hashtable();
-    else
-      fr.featureGroups.clear();
 
-    allFeatures = new Hashtable();
-    SequenceFeature[] features;
+    Vector allFeatures = new Vector();
+    Vector allGroups = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group;
 
-  for (int i = 0; i < av.alignment.getHeight(); i++)
-  {
-    features = av.alignment.getSequenceAt(i).getDatasetSequence().
-        getSequenceFeatures();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
+        continue;
 
-    if (features == null)
-      continue;
+      alignmentHasFeatures = true;
 
-    int index = 0;
-    while (index < features.length)
-    {
-      if(features[index].getFeatureGroup()!=null
-          && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))
+      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(features[index].getFeatureGroup(), new Boolean(true));
-         if(groupPanel==null)
-            groupPanel = new JPanel();
-
-          final JCheckBox check = new JCheckBox(features[index].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();
-                  }
-                  resetTable();
-                }
-              });
-          groupPanel.add(check);
+           allFeatures.addElement(tmpfeatures[index].getType());
        }
-      if (!allFeatures.contains(features[index].getType()))
-      {
-        if(features[index].featureGroup!=null)
-          allFeatures.put(features[index].getType(), features[index].featureGroup);
-        else
-          allFeatures.put(features[index].getType(), "NOGROUP");
-      }
-      index++;
+       index ++;
     }
   }
-    if(allFeatures.size()<1)
+
+
+    if(!alignmentHasFeatures)
      {
        try
        { frame.setClosed(true);  }
@@ -207,60 +225,81 @@ public class FeatureSettings extends JPanel
        return;
      }
 
-     resetTable();
+     resetTable(false);
   }
 
-  void resetTable()
+  void resetTable(boolean groupsChanged)
   {
-    int fSize = allFeatures.size();
+   SequenceFeature [] tmpfeatures;
+   String group=null, type;
+   Vector visibleChecks = new Vector();
 
-    String type;
-    boolean originalExists = false;
-    if (originalData != null)
-      originalExists = true;
-    else
-      originalData = new Object[fSize][3];
+   //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;
 
-    Object[][] tmp = new Object[fSize][3];
-    int tmpIndex = 0;
+        tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+        int index = 0;
+        while (index < tmpfeatures.length)
+        {
+          group = tmpfeatures[index].featureGroup;
 
-    Enumeration en = allFeatures.keys();
-    int i=0;
-    while(en.hasMoreElements())
-    {
-      type = en.nextElement().toString();
-      Color col = fr.getColour(type);
+          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];
+    int dataIndex = 0;
 
-      //This will ignore any features which are in groups not shown
-     Object visibleGroup =  fr.featureGroups.get(allFeatures.get(type));
-     if(visibleGroup == null
-           || ((Boolean)(visibleGroup)).booleanValue())
+    if(fr.renderOrder!=null)
+    {
+      //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--)
       {
-        tmp[tmpIndex][0] = type;
-        tmp[tmpIndex][1] = col;
-        if (av.featuresDisplayed != null)
-          tmp[tmpIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
-        else
-          tmp[tmpIndex][2] = new Boolean(true);
-
-        tmpIndex++;
-      }
+           type = fr.renderOrder[ro];
 
+           if(!visibleChecks.contains(type))
+             continue;
 
-      if (!originalExists)
-      {
-        originalData[i][0] = type;
-        originalData[i][1] = col;
-        if (av.featuresDisplayed != null)
-          originalData[i][2] = new Boolean(av.featuresDisplayed.contains(type));
-        else
-          originalData[i][2] = new Boolean(true);
+           data[dataIndex][0] = type;
+           data[dataIndex][1] = fr.getColour(type);
+           data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
+           dataIndex++;
+           visibleChecks.removeElement(type);
       }
-      i++;
     }
 
-    Object [][]data = new Object[tmpIndex][3];
-    System.arraycopy(tmp, 0, data,0, tmpIndex);
+    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);
@@ -431,6 +470,11 @@ public class FeatureSettings extends JPanel
             return data;
           }
 
+          public void setData(Object[][] data)
+          {
+            this.data = data;
+          }
+
           public int getColumnCount() {
               return columnNames.length;
           }