X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=003200d754eedbd6406fc6797773305026754e36;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=6e38f1b9eabfb7788d78e4ecba5547283e7b7224;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6e38f1b..003200d 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,71 +1,730 @@
+/*
+ * 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.gui;
 
 import jalview.datamodel.*;
-import jalview.schemes.*;
+
 import java.awt.*;
+
 import java.util.*;
 
-public class FeatureRenderer implements RendererI
+import java.awt.image.*;
+import javax.swing.*;
+import javax.swing.JOptionPane;
+import java.awt.event.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
 {
-  AlignViewport av;
+    AlignViewport av;
+    Color resBoxColour;
+    float transparency = 1.0f;
+    FontMetrics fm;
+    int charOffset;
 
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
+    Hashtable featureColours = new Hashtable();
 
-  public FeatureRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
 
+    // A higher level for grouping features of a
+   // particular type
+    Hashtable featureGroups = null;
+
+    // This is actually an Integer held in the hashtable,
+    // Retrieved using the key feature type
+    Object currentColour;
+
+    String [] renderOrder;
+
+    /**
+     * Creates a new FeatureRenderer object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public FeatureRenderer(AlignViewport av)
+    {
+        this.av = av;
+    }
+
+    public void transferSettings(FeatureRenderer fr)
+    {
+      renderOrder = fr.renderOrder;
+      featureGroups = fr.featureGroups;
+      featureColours = fr.featureColours;
+      transparency =  fr.transparency;
+    }
+
+    BufferedImage offscreenImage;
+    boolean offscreenRender = false;
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+    {
+      return new Color( findFeatureColour (initialCol.getRGB(),
+                        seq, res ));
+    }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
-  {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-    while( e.hasMoreElements() )
+    /**
+     * This is used by the Molecule Viewer and Overview to
+     * get the accurate colourof the rendered sequence
+     */
+    public int findFeatureColour(int initialCol, SequenceI seq, int column)
     {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      int fstart = seq.findIndex(sf.getStart())-1;
-      int fend = seq.findIndex(sf.getEnd())-1;
+      if(!av.showSequenceFeatures)
+        return initialCol;
 
-      if(    (fstart>=start&&fstart<=end) || (fend>=start&&fend<=end))
+      if(seq!=lastSeq)
+      {
+        lastSeq = seq;
+        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
+
+        sfSize = sequenceFeatures.length;
+      }
+
+      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
+        return Color.white.getRGB();
+
+
+      //Only bother making an offscreen image if transparency is applied
+      if(transparency!=1.0f && offscreenImage==null)
+      {
+        offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
+      }
+
+      currentColour = null;
+
+      offscreenRender = true;
+
+      if(offscreenImage!=null)
+      {
+        offscreenImage.setRGB(0,0,initialCol);
+        drawSequence(offscreenImage.getGraphics(),
+                     lastSeq,
+                     column,column,0);
+
+        return offscreenImage.getRGB(0,0);
+      }
+      else
       {
-        if(fstart==fend)
+        drawSequence(null,
+                    lastSeq,
+                    lastSeq.findPosition(column),
+                    -1, -1);
+
+        if (currentColour == null)
+          return initialCol;
+        else
+          return  ((Integer)currentColour).intValue();
+      }
+
+
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+   // String type;
+   // SequenceFeature sf;
+    SequenceI lastSeq;
+    SequenceFeature [] sequenceFeatures;
+    int sfSize, sfindex, spos, epos;
+
+    public void drawSequence(Graphics g, SequenceI seq,
+                             int start, int end, int y1)
+    {
+      if ( seq.getDatasetSequence().getSequenceFeatures() == null
+          || seq.getDatasetSequence().getSequenceFeatures().length==0)
+        return;
+
+      if(g!=null)
+        fm = g.getFontMetrics();
+
+
+      if (av.featuresDisplayed == null
+          || renderOrder==null
+          || newFeatureAdded)
+       {
+         findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
+
+         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+         sfSize = sequenceFeatures.length;
+       }
+
+       if(lastSeq==null || seq!=lastSeq)
+      {
+        lastSeq = seq;
+        sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+        sfSize = sequenceFeatures.length;
+      }
+
+
+      if (transparency != 1 && g!=null)
+      {
+        Graphics2D g2 = (Graphics2D) g;
+        g2.setComposite(
+            AlphaComposite.getInstance(
+                AlphaComposite.SRC_OVER, transparency));
+      }
+
+      if(!offscreenRender)
+      {
+        spos = lastSeq.findPosition(start);
+        epos = lastSeq.findPosition(end);
+      }
+
+
+      String type;
+      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
+       {
+        type =  renderOrder[renderIndex];
+
+        if(type==null || !av.featuresDisplayed.containsKey(type))
+          continue;
+
+        // loop through all features in sequence to find
+        // current feature to render
+        for (sfindex = 0; sfindex < sfSize; sfindex++)
         {
-          g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
-          g.setColor(Color.white);
+          if(sequenceFeatures.length<=sfindex)
+          {
+            continue;
+          }
+          if (!sequenceFeatures[sfindex].type.equals(type))
+            continue;
+
+          if (featureGroups != null
+              && sequenceFeatures[sfindex].featureGroup != null
+              &&
+              featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+              &&
+              ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
+              booleanValue())
+          {
+            continue;
+          }
+
+          if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
+                            || sequenceFeatures[sfindex].getEnd() < spos))
+            continue;
+
+          if (offscreenRender && offscreenImage==null)
+          {
+            if (sequenceFeatures[sfindex].begin <= start &&
+                sequenceFeatures[sfindex].end  >= start)
+            {
+              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                 type);
+            }
+          }
+          else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+          {
+
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          new Color( ( (Integer) av.featuresDisplayed.get(
+                sequenceFeatures[sfindex].type)).intValue()),
+                          start, end, y1);
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          new Color( ( (Integer) av.featuresDisplayed.get(
+                sequenceFeatures[sfindex].type)).intValue()),
+                          start, end, y1);
+
+          }
+          else
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          getColour(sequenceFeatures[sfindex].type),
+                          start, end, y1);
 
-          char s = seq.getSequence().charAt(fstart);
-          FontMetrics fm = g.getFontMetrics();
-          int charOffset =  (width - fm.charWidth(s))/2;
-          int pady = height/5;
-          g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);
 
         }
-        else
+
+      }
+
+        if(transparency!=1.0f && g!=null)
+        {
+          Graphics2D g2 = (Graphics2D) g;
+          g2.setComposite(
+              AlphaComposite.getInstance(
+                  AlphaComposite.SRC_OVER, 1.0f));
+        }
+    }
+
+
+    char s;
+    int i;
+    void renderFeature(Graphics g, SequenceI seq,
+                       int fstart, int fend, Color featureColour, int start, int end,  int y1)
+    {
+
+      if (((fstart <= end) && (fend >= start)))
+      {
+        if (fstart < start)
+        { // fix for if the feature we have starts before the sequence start,
+          fstart = start; // but the feature end is still valid!!
+        }
+
+        if (fend >= end)
         {
-          for (int i = fstart; i <= fend; i++)
+          fend = end;
+        }
+          int pady = (y1 + av.charHeight) - av.charHeight / 5;
+          for (i = fstart; i <= fend; i++)
           {
-            g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
+            s = seq.getCharAt(i);
+
+            if (jalview.util.Comparison.isGap(s))
+            {
+              continue;
+            }
+
+            g.setColor(featureColour);
+
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
+
+            if(offscreenRender || !av.validCharWidth)
+              continue;
 
             g.setColor(Color.white);
-            char s = seq.getSequence().charAt(i);
-            FontMetrics fm = g.getFontMetrics();
-            int charOffset = (width - fm.charWidth(s)) / 2;
-            int pady = height / 5;
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
             g.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i-start),
-                         y1 + height - pady);
+                         charOffset + (av.charWidth * (i - start)),
+                         pady);
+
+          }
+      }
+    }
+
+
+    boolean newFeatureAdded = false;
+
+    public void featuresAdded()
+    {
+      findAllFeatures();
+    }
+
+   boolean findingFeatures = false;
+   synchronized void findAllFeatures()
+   {
+      newFeatureAdded = false;
+
+      if(findingFeatures)
+      {
+        newFeatureAdded = true;
+        return;
+      }
+
+      findingFeatures = true;
+      jalview.schemes.UserColourScheme ucs = new
+          jalview.schemes.UserColourScheme();
+
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
+
+      av.featuresDisplayed.clear();
+
+      Vector allfeatures = new Vector();
+      for (int i = 0; i < av.alignment.getHeight(); i++)
+      {
+        SequenceFeature [] features
+            = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+
+        if (features == null)
+          continue;
+
+        int index = 0;
+        while (index < features.length)
+        {
+          if (!av.featuresDisplayed.containsKey(features[index].getType()))
+          {
+            if(!(features[index].begin == 0 && features[index].end ==0))
+            {
+              // If beginning and end are 0, the feature is for the whole sequence
+              // and we don't want to render the feature in the normal way
+
+              if (getColour(features[index].getType()) == null)
+              {
+                 featureColours.put(features[index].getType(),
+                                   ucs.createColourFromName(features[index].
+                    getType()));
+              }
+
+              av.featuresDisplayed.put(features[index].getType(),
+                                       new Integer(getColour(features[index].
+                  getType()).getRGB()));
+              allfeatures.addElement(features[index].getType());
+            }
+          }
+          index++;
+        }
+      }
+
+      renderOrder = new String[allfeatures.size()];
+      Enumeration en = allfeatures.elements();
+      int i = allfeatures.size()-1;
+      while(en.hasMoreElements())
+      {
+        renderOrder[i] = en.nextElement().toString();
+        i--;
+      }
+
+      findingFeatures = false;
+    }
+
+    public Color getColour(String featureType)
+    {
+      Color colour = (Color)featureColours.get(featureType);
+      return colour;
+    }
+
+
+    static String lastFeatureAdded;
+    static String lastFeatureGroupAdded;
+    static String lastDescriptionAdded;
+
+    public boolean createNewFeatures(SequenceI[] sequences,
+                                  SequenceFeature [] features)
+    {
+      return amendFeatures(sequences, features, true, null);
+    }
+
+    int featureIndex = 0;
+    boolean amendFeatures(final SequenceI[] sequences,
+                          final SequenceFeature[] features,
+                          boolean newFeatures,
+                          final AlignmentPanel ap)
+    {
+      JPanel bigPanel = new JPanel(new BorderLayout());
+      final JComboBox name = new JComboBox();
+      final JComboBox source = new JComboBox();
+      final JTextArea description = new JTextArea(3,25);
+      final JSpinner start = new JSpinner();
+      final JSpinner end = new JSpinner();
+      start.setPreferredSize(new Dimension(80,20));
+      end.setPreferredSize(new Dimension(80,20));
+      final JPanel colour = new JPanel();
+      colour.setBorder(BorderFactory.createEtchedBorder());
+      colour.setMaximumSize(new Dimension(40,10));
+      colour.addMouseListener(new MouseAdapter()
+          {
+            public void mousePressed(MouseEvent evt)
+            {
+              colour.setBackground(
+                  JColorChooser.showDialog(Desktop.desktop,
+                                           "Select Feature Colour",
+                                           colour.getBackground()));
+            }
+          });
+
+      JPanel panel = new JPanel(new GridLayout(3, 2));
+      panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));
+      panel.add(name);
+      panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
+      panel.add(source);
+      panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
+      JPanel tmp = new JPanel();
+      tmp.add(colour);
+      colour.setPreferredSize(new Dimension(150,15));
+      panel.add(tmp);
+      name.setEditable(true);
+      source.setEditable(true);
+
+      bigPanel.add(panel, BorderLayout.NORTH);
+      panel = new JPanel();
+      panel.add(new JLabel("Description: ", JLabel.RIGHT));
+      description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+      description.setLineWrap(true);
+      panel.add(new JScrollPane(description));
+
+      if(!newFeatures)
+      {
+        bigPanel.add(panel, BorderLayout.SOUTH);
+
+        panel = new JPanel();
+        panel.add(new JLabel(" Start:", JLabel.RIGHT));
+        panel.add(start);
+        panel.add(new JLabel("  End:", JLabel.RIGHT));
+        panel.add(end);
+        bigPanel.add(panel, BorderLayout.CENTER);
+      }
+      else
+        bigPanel.add(panel, BorderLayout.CENTER);
+
+      if (lastFeatureAdded == null)
+        if (features[0].type != null)
+          lastFeatureAdded = features[0].type;
+        else
+          lastFeatureAdded = "feature_1";
+
+      if (lastFeatureGroupAdded == null)
+        if (features[0].featureGroup != null)
+          lastFeatureGroupAdded = features[0].featureGroup;
+        else
+          lastFeatureAdded = "Jalview";
 
+
+      Enumeration en;
+      if (featureGroups != null)
+      {
+        en = featureGroups.keys();
+        while (en.hasMoreElements())
+        {
+          source.addItem(en.nextElement().toString());
+        }
+      }
+
+      if (newFeatures)
+      {
+        if(av.featuresDisplayed != null)
+        {
+          en = av.featuresDisplayed.keys();
+          while (en.hasMoreElements())
+          {
+            name.addItem(en.nextElement().toString());
           }
         }
+
+        name.setSelectedItem(lastFeatureAdded);
+        source.setSelectedItem(lastFeatureGroupAdded);
+        description.setText(
+            lastDescriptionAdded == null ?
+            features[0].description : lastDescriptionAdded);
+
+        if (getColour(lastFeatureAdded) != null)
+        {
+          colour.setBackground(getColour(lastFeatureAdded));
+        }
+        else
+        {
+          colour.setBackground(new Color(60, 160, 115));
+        }
+
       }
+      else if (!newFeatures)
+      {
+        featureIndex = 0;
+        for(int f=0; f<features.length; f++)
+        {
+          name.addItem(features[f].getType().toString());
+        }
+
+        description.setText(features[0].getDescription());
+        source.setSelectedItem(features[0].getFeatureGroup());
+        start.setValue(new Integer(features[0].getBegin()));
+        end.setValue(new Integer(features[0].getEnd()));
+        colour.setBackground(
+                getColour(name.getSelectedItem().toString()));
+        name.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            int index = name.getSelectedIndex();
+            if(index!=-1)
+            {
+              featureIndex = index;
+              description.setText(features[index].getDescription());
+              source.setSelectedItem(features[index].getFeatureGroup());
+              start.setValue(new Integer(features[index].getBegin()));
+              end.setValue(new Integer(features[index].getEnd()));
+              colour.setBackground(
+                  getColour(name.getSelectedItem().toString()));
+
+              SearchResults highlight = new SearchResults();
+              highlight.addResult(sequences[0],
+                                  features[index].getBegin(),
+                                  features[index].getEnd());
+
+              ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+            }
+            Color col = getColour(name.getSelectedItem().toString());
+            if (col == null)
+              col = new
+                  jalview.schemes.UserColourScheme()
+                  .createColourFromName(name.getSelectedItem().toString());
+
+            colour.setBackground(col);
+          }
+        });
 
+      }
+
+
+      Object [] options;
+      if(!newFeatures)
+        options = new Object[]{"Amend", "Delete", "Cancel"};
+      else
+        options = new Object[]{"OK", "Cancel"};
+
+      String title = newFeatures ?  "Create New Sequence Feature(s)" :
+                                    "Amend/Delete Features for "
+                                    +sequences[0].getName();
+
+      int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+                                                   bigPanel,
+                                                   title,
+                                                   JOptionPane.YES_NO_CANCEL_OPTION,
+                                                   JOptionPane.QUESTION_MESSAGE,
+                                                   null,
+                                                   options, "OK");
+
+      jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+      if (reply == JOptionPane.OK_OPTION
+          && name.getSelectedItem() != null
+          && source.getSelectedItem() != null)
+      {
+        lastFeatureAdded = name.getSelectedItem().toString();
+        lastFeatureGroupAdded = source.getSelectedItem().toString();
+        lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+      }
+
+      if(!newFeatures)
+      {
+        SequenceFeature sf = features[featureIndex];
+
+        if(reply==JOptionPane.NO_OPTION)
+          sequences[0].getDatasetSequence().deleteFeature(sf);
+        else if(reply==JOptionPane.YES_OPTION)
+        {
+          sf.type = lastFeatureAdded;
+          sf.featureGroup = lastFeatureGroupAdded;
+          sf.description = lastDescriptionAdded;
+          setColour(sf.type, colour.getBackground());
+          try{
+            sf.begin = ((Integer)start.getValue()).intValue();
+            sf.end = ((Integer)end.getValue()).intValue();
+          }catch(NumberFormatException ex)
+          {}
+
+          ffile.parseDescriptionHTML(sf, false);
+        }
+      }
+      else
+      {
+        if (reply == JOptionPane.OK_OPTION
+            && name.getSelectedItem() != null
+            && source.getSelectedItem() != null)
+        {
+          for (int i = 0; i < sequences.length; i++)
+          {
+            features[i].type = lastFeatureAdded;
+            features[i].featureGroup = lastFeatureGroupAdded;
+            features[i].description = lastDescriptionAdded;
+            sequences[i].addSequenceFeature(features[i]);
+            ffile.parseDescriptionHTML(features[i], false);
+          }
+
+          if (av.featuresDisplayed == null)
+            av.featuresDisplayed = new Hashtable();
+
+          if (featureGroups == null)
+            featureGroups = new Hashtable();
+
+          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+
+          Color col = colour.getBackground();
+          setColour(lastFeatureAdded, colour.getBackground());
+
+          av.featuresDisplayed.put(lastFeatureGroupAdded,
+                                   new Integer(col.getRGB()));
+
+          findAllFeatures();
+
+          return true;
+        }
+        else
+          return false;
+      }
+
+      if(name.getSelectedIndex()==-1)
+        findAllFeatures();
+
+
+      return true;
+    }
+
+    public void setColour(String featureType, Color col)
+    {
+      featureColours.put(featureType, col);
+    }
+
+    public void setTransparency(float value)
+    {
+      transparency = value;
+    }
+
+    public float getTransparency()
+    {
+      return transparency;
     }
-   }
+
+    public void setFeaturePriority(Object [][] data)
+    {
+      // The feature table will display high priority
+      // features at the top, but theses are the ones
+      // we need to render last, so invert the data
+      if(av.featuresDisplayed!=null)
+        av.featuresDisplayed.clear();
+      else
+        av.featuresDisplayed = new Hashtable();
+
+      renderOrder = new String[data.length];
+
+      if (data.length > 0)
+        for (int i = 0; i < data.length; i++)
+        {
+          String type = data[i][0].toString();
+          setColour(type, (Color) data[i][1]);
+          if ( ( (Boolean) data[i][2]).booleanValue())
+          {
+            av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+          }
+
+          renderOrder[data.length - i - 1] = type;
+        }
+
+    }
+
+
+
 
 }