X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=ad9ad1dd3f49f7f1ffd15f43cee105b1bb814315;hb=e3eb93bc131a0f088312fddde91b728dbebe40d4;hp=532518055cb689c1996d07b18a60b9a2a08053c4;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 5325180..ad9ad1d 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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.gui;
 
 import jalview.datamodel.*;
@@ -10,220 +28,300 @@ import java.awt.event.*;
 import javax.swing.table.*;
 import java.io.*;
 import jalview.io.JalviewFileChooser;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Color;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
 public class FeatureSettings extends JPanel
 {
+  DasSourceBrowser dassourceBrowser;
+  JPanel settingsPane = new JPanel();
+  JPanel dasSettingsPane = new JPanel();
 
   final FeatureRenderer fr;
-  final AlignmentPanel ap;
-  final AlignViewport av;
+  final AlignFrame af;
   Object [][] originalData;
   final JInternalFrame frame;
   JScrollPane scrollPane = new JScrollPane();
   JTable table;
+  JPanel groupPanel;
+  JSlider transparency = new JSlider();
 
-  public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
+  JPanel transPanel = new JPanel(new FlowLayout());
+  boolean alignmentHasFeatures = false;
+
+  public FeatureSettings(AlignFrame af)
   {
-    this.ap = ap;
-    this.av = av;
-    fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
-    av.alignment.getSequences();
+    this.af = af;
+    fr = af.getFeatureRenderer();
+
+    transparency.setMaximum( 100 - (int)(fr.transparency*100) ) ;
+
+   try
+   {
+     jbInit();
+   }
+   catch (Exception ex)
+   {
+     ex.printStackTrace();
+   }
+
+    dassourceBrowser = new DasSourceBrowser();
+    dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
+
+
+
+    if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null)
+       fr.findAllFeatures();
+
+
+    setTableData();
+
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);
+    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+  }
 
-    setTableData();
+  public void setTableData()
+  {
+    alignmentHasFeatures = false;
 
-    final JSlider transparency = new JSlider(0, 70, 0);
-    transparency.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
-        ap.repaint();
-      }
-    });
+    if (fr.featureGroups == null)
+      fr.featureGroups = new Hashtable();
 
-    JPanel transPanel = new JPanel(new FlowLayout());
-    transPanel.add(new JLabel("Transparency"));
-    transPanel.add(transparency);
+    Vector allFeatures = new Vector();
+    Vector allGroups = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group;
 
-    //////////////////////////////////////////////
-    //We're going to need those OK cancel buttons
-    JPanel buttonPanel = new JPanel(new FlowLayout());
-    JButton button = new JButton("OK");
-    button.addActionListener(new ActionListener()
+    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
     {
-      public void actionPerformed(ActionEvent evt)
+      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
+        continue;
+
+      alignmentHasFeatures = true;
+
+      tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+
+      int index = 0;
+      while (index < tmpfeatures.length)
       {
-        try
+        if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)
         {
-          frame.setClosed(true);
+          index++;
+          continue;
         }
-        catch (Exception exe)
-        {}
-      }
-    });
-    buttonPanel.add(button);
-    button = new JButton("Cancel");
-    button.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        try
+
+        if(tmpfeatures[index].getFeatureGroup()!=null)
         {
-          updateFeatureRenderer(originalData);
-          frame.setClosed(true);
-        }
-        catch (Exception exe)
-        {}
-      }
-    });
-    buttonPanel.add(button);
+          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();
+             }
+             else
+             {
+               fr.featureGroups.put(group, new Boolean(visible));
+               if (groupPanel == null)
+               {
+                 groupPanel = new JPanel();
+               }
 
-    button = new JButton("Load Colours");
-    button.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        load();
-      }
-    });
-    buttonPanel.add(button);
-    button = new JButton("Save Colours");
-    button.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        save();
-      }
-    });
-    buttonPanel.add(button);
+               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(true);
+                 }
+               });
+               groupPanel.add(check);
+             }
+           }
+
+       }
 
-    this.setLayout(new BorderLayout());
-    JPanel bigPanel = new JPanel(new BorderLayout());
-    bigPanel.add(transPanel, BorderLayout.SOUTH);
-    bigPanel.add(scrollPane, BorderLayout.CENTER);
+       if (!allFeatures.contains(tmpfeatures[index].getType()))
+       {
+           allFeatures.addElement(tmpfeatures[index].getType());
+       }
+       index ++;
+    }
+  }
 
-    add(bigPanel, BorderLayout.CENTER);
-    add(buttonPanel, BorderLayout.SOUTH);
 
+    if(!alignmentHasFeatures)
+     {
+    //   try
+     //  { frame.setClosed(true);  }
+    //   catch (Exception ex){}
+
+    //   JOptionPane.showInternalMessageDialog(
+    ///       Desktop.desktop, "No features have been added to this alignment!",
+    //
+   //    return;
+     }
 
+     resetTable(false);
   }
 
-  void setTableData()
+
+  void resetTable(boolean groupsChanged)
   {
-    Vector allFeatures = new Vector();
-    Vector features;
-    Enumeration e;
-    SequenceFeature sf;
+   SequenceFeature [] tmpfeatures;
+   String group=null, type;
+   Vector visibleChecks = new Vector();
 
-    for(int i=0; i< av.alignment.getHeight(); i++)
+   //Find out which features should be visible depending on which groups
+   //are selected / deselected
+    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
     {
-       features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-       if(features==null)
-         continue;
 
-       e = features.elements();
-       while(e.hasMoreElements())
-       {
-         sf = (SequenceFeature)e.nextElement();
-         if(!allFeatures.contains(sf.getType()))
-         {
-           allFeatures.addElement(sf.getType());
-         }
-       }
-    }
-    if(allFeatures.size()<1)
-     {
-       try{
-         frame.setClosed(true);
-       }catch(Exception ex){}
-       return;
-     }
+        tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+        if (tmpfeatures == null)
+          continue;
 
-    int fSize = allFeatures.size();
+        int index = 0;
+        while (index < tmpfeatures.length)
+        {
+          group = tmpfeatures[index].featureGroup;
 
-    String type;
-    boolean originalExists = false;
-    if(originalData!=null)
-      originalExists = true;
-    else
-      originalData = new Object[fSize][3];
+          if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0)
+          {
+            index ++;
+            continue;
+          }
+
+          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(af.getViewport().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++;
+    }
 
-        table.getColumnModel().getColumn(0).setPreferredWidth(200);
+    if(originalData==null)
+    {
+      originalData = new Object[data.length][3];
+      System.arraycopy(data,0,originalData,0,data.length);
+    }
 
-        table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    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.addMouseListener(new MouseAdapter()
-            {
-              public void mousePressed(MouseEvent evt)
-              {
-                selectedRow = table.rowAtPoint(evt.getPoint());
-              }
-            });
+    table.setDefaultEditor(Color.class,
+                      new ColorEditor());
 
-        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.getColumnModel().getColumn(0).setPreferredWidth(200);
+
+    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+    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;
+            }
+          }
+    });
+
+    if (groupPanel != null)
+    {
+      groupPanel.setLayout(
+          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+
+      groupPanel.validate();
+      bigPanel.add(groupPanel, BorderLayout.NORTH);
+    }
+
+    updateFeatureRenderer(data);
+
   }
 
   void load()
@@ -258,11 +356,11 @@ public class FeatureSettings extends JPanel
          }
 
          setTableData();
-         ap.repaint();
+         af.alignPanel.repaint();
        }
        catch (Exception ex)
        {
-         System.out.println("Error loading User ColourFile\n" + ex);
+         System.out.println("Error loading User Colour File\n" + ex);
        }
      }
   }
@@ -291,8 +389,6 @@ public class FeatureSettings extends JPanel
             Enumeration e = fr.featureColours.keys();
            while(e.hasMoreElements())
            {
-
-
                 jalview.binding.Colour col = new jalview.binding.Colour();
                 col.setName(e.nextElement().toString());
                 col.setRGB(jalview.util.Format.getHexString(
@@ -308,17 +404,197 @@ public class FeatureSettings extends JPanel
             ex.printStackTrace();
         }
     }
+  }
+
+  public void invertSelection()
+  {
+    for(int i=0; i<table.getRowCount(); i++)
+    {
+      Boolean value = (Boolean)table.getValueAt(i,2);
+
+      table.setValueAt(
+          new Boolean(!value.booleanValue()),
+                       i,2);
+    }
+  }
+
+  public void close()
+  {
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception exe)
+    {}
 
   }
 
   public void updateFeatureRenderer(Object [][] data)
   {
     fr.setFeaturePriority( data );
-    ap.repaint();
+    af.alignPanel.repaint();
+
+    if(af.alignPanel.overviewPanel!=null)
+      af.alignPanel.overviewPanel.updateOverviewImage();
   }
 
   int selectedRow =-1;
+  JTabbedPane tabbedPane = new JTabbedPane();
+  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout2 = new BorderLayout();
+  BorderLayout borderLayout3 = new BorderLayout();
+  JPanel bigPanel = new JPanel();
+  BorderLayout borderLayout4 = new BorderLayout();
+  JButton invert = new JButton();
+  JPanel buttonPanel = new JPanel();
+  JButton cancel = new JButton();
+  JButton ok = new JButton();
+  JButton loadColours = new JButton();
+  JButton saveColours = new JButton();
+  JPanel dasButtonPanel = new JPanel();
+  JButton fetchDAS = new JButton();
+  JButton saveDAS = new JButton();
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    settingsPane.setLayout(borderLayout2);
+    dasSettingsPane.setLayout(borderLayout3);
+    bigPanel.setLayout(borderLayout4);
+    invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    invert.setText("Invert Selection");
+    invert.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertSelection();
+      }
+    });
+    cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+          updateFeatureRenderer(originalData);
+          close();
+      }
+    });
+    ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        close();
+      }
+    });
+    loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    loadColours.setText("Load Colours");
+    loadColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        load();
+      }
+    });
+    saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    saveColours.setText("Save Colours");
+    saveColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        save();
+      }
+    });
+    transparency.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
+        af.alignPanel.repaint();
+      }
+    });
+
+
+    transparency.setMaximum(70);
+    fetchDAS.setText("Fetch DAS Features");
+    fetchDAS.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchDAS_actionPerformed(e);
+      }
+    });
+    saveDAS.setText("Save as default");
+    saveDAS.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveDAS_actionPerformed(e);
+      }
+    });
+    dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
+    dasSettingsPane.setBorder(null);
+    this.add(tabbedPane, java.awt.BorderLayout.CENTER);
+    tabbedPane.addTab("Display Settings", settingsPane );
+    tabbedPane.addTab("DAS Settings", dasSettingsPane);
+    bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
+    transPanel.add(transparency);
+    transPanel.add(invert);
+    buttonPanel.add(ok);
+    buttonPanel.add(cancel);
+    buttonPanel.add(loadColours);
+    buttonPanel.add(saveColours);
+    bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
+    dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
+    dasButtonPanel.add(fetchDAS);
+    dasButtonPanel.add(saveDAS);
+    settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
+    settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
+  }
+
+  public void fetchDAS_actionPerformed(ActionEvent e)
+  {
+    Vector selectedSources = dassourceBrowser.getSelectedSources();
+
+    SequenceI [] dataset, seqs ;
+    int iSize;
 
+    if(af.getViewport().getSelectionGroup()!=null
+      && af.getViewport().getSelectionGroup().getSize(false)>0)
+    {
+      iSize = af.getViewport().getSelectionGroup().getSize(false);
+      dataset = new SequenceI[iSize];
+      seqs = af.getViewport().getSelectionGroup().
+          getSequencesInOrder(
+              af.getViewport().getAlignment());
+    }
+    else
+    {
+       iSize = af.getViewport().getAlignment().getHeight();
+       seqs = af.getViewport().getAlignment().getSequencesArray();
+    }
+
+    dataset = new SequenceI[iSize];
+    for (int i = 0; i < iSize; i++)
+    {
+      dataset[i] = seqs[i].getDatasetSequence();
+    }
+
+    new jalview.io.DasSequenceFeatureFetcher(
+        dataset,
+        af,
+        selectedSources);
+
+    af.getViewport().setShowSequenceFeatures(true);
+    af.showSeqFeatures.setSelected(true);
+  }
+
+  public void saveDAS_actionPerformed(ActionEvent e)
+  {
+    dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);
+  }
 
   /////////////////////////////////////////////////////////////////////////
   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
@@ -339,6 +615,11 @@ public class FeatureSettings extends JPanel
             return data;
           }
 
+          public void setData(Object[][] data)
+          {
+            this.data = data;
+          }
+
           public int getColumnCount() {
               return columnNames.length;
           }