X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=c90fb475d7d1dde0dd1bbc05e48d25b78bf6c9b4;hb=94e19634c669879ab63bbb82d5489c200cdb18f8;hp=a8412f0d1137f541de1c67dee9dbfc5fe08bdf4f;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index a8412f0..c90fb47 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,79 +1,752 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.appletgui;
 
-import jalview.datamodel.*;
-import java.awt.*;
 import java.util.*;
 
+import java.awt.*;
+
+import java.awt.event.*;
+
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class FeatureRenderer
 {
   AlignViewport av;
 
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
+  Hashtable featureColours = new Hashtable();
+
+  // A higher level for grouping features of a
+  // particular type
+  Hashtable featureGroups = null;
 
+  // Holds web links for feature groups and feature types
+  // in the form label|link
+  Hashtable featureLinks = null;
+
+  // This is actually an Integer held in the hashtable,
+  // Retrieved using the key feature type
+  Object currentColour;
+
+  String[] renderOrder;
+
+  FontMetrics fm;
+  int charOffset;
+
+  float transparency = 1f;
+
+  TransparencySetter transparencySetter = null;
+
+  /**
+   * Creates a new FeatureRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
   public FeatureRenderer(AlignViewport av)
   {
     this.av = av;
+
+    if (!System.getProperty("java.version").startsWith("1.1"))
+    {
+      transparencySetter = new TransparencySetter();
+    }
   }
 
+  public void transferSettings(FeatureRenderer fr)
+  {
+    renderOrder = fr.renderOrder;
+    featureGroups = fr.featureGroups;
+    featureColours = fr.featureColours;
+    transparency = fr.transparency;
+  }
+
+
+  static String lastFeatureAdded;
+  static String lastFeatureGroupAdded;
+  static String lastDescriptionAdded;
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
+  int featureIndex = 0;
+  boolean deleteFeature = false;
+  Panel colourPanel;
+  boolean amendFeatures(final SequenceI[] sequences,
+                        final SequenceFeature[] features,
+                        boolean newFeatures,
+                        final AlignmentPanel ap)
   {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-    while( e.hasMoreElements() )
+    Panel bigPanel = new Panel(new BorderLayout());
+    final TextField name = new TextField(16);
+    final TextField source = new TextField(16);
+    final TextArea description = new TextArea(3, 35);
+    final TextField start = new TextField(8);
+    final TextField end = new TextField(8);
+    final Choice overlaps;
+    Button deleteButton = new Button("Delete");
+    deleteFeature = false;
+
+    colourPanel = new Panel(null);
+    colourPanel.setSize(110,15);
+    final FeatureRenderer fr = this;
+
+    Panel panel = new Panel(new GridLayout(3, 1));
+
+    Panel tmp;
+
+    ///////////////////////////////////////
+    ///MULTIPLE FEATURES AT SELECTED RESIDUE
+    if(!newFeatures && features.length>1)
     {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      if(sf.getStart()>seq.getEnd())
-        continue;
+     panel = new Panel(new GridLayout(4, 1));
+     tmp = new Panel();
+     tmp.add(new Label("Select Feature: "));
+     overlaps = new Choice();
+     for(int i=0; i<features.length; i++)
+     {
+       String item = features[i].getType()
+        +"/"+features[i].getBegin()+"-"+features[i].getEnd();
+
+       if(features[i].getFeatureGroup()!=null)
+         item += " ("+features[i].getFeatureGroup()+")";
+
+       overlaps.addItem(item);
+     }
+
+     tmp.add(overlaps);
+
+     overlaps.addItemListener(new java.awt.event.ItemListener()
+     {
+       public void itemStateChanged(java.awt.event.ItemEvent e)
+       {
+         int index = overlaps.getSelectedIndex();
+         if (index != -1)
+         {
+           featureIndex = index;
+           name.setText(features[index].getType());
+           description.setText(features[index].getDescription());
+           source.setText(features[index].getFeatureGroup());
+           start.setText(features[index].getBegin()+"");
+           end.setText(features[index].getEnd()+"");
+
+           SearchResults highlight = new SearchResults();
+           highlight.addResult(sequences[0],
+                               features[index].getBegin(),
+                               features[index].getEnd());
+
+           ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+         }
+         Color col = getColour(name.getText());
+         if (col == null)
+         {
+           col = new
+               jalview.schemes.UserColourScheme()
+               .createColourFromName(name.getText());
+         }
 
-      int fstart = seq.findIndex(sf.getStart())-1;
-      int fend = seq.findIndex(sf.getEnd())-1;
+         colourPanel.setBackground(col);
+       }
+     });
 
-      if(   (fstart<=end && fend>=start)  )
+
+     panel.add(tmp);
+    }
+    //////////
+    //////////////////////////////////////
+
+
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Name: ", Label.RIGHT));
+    tmp.add(name);
+
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Group: ",Label.RIGHT));
+    tmp.add(source);
+
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Colour: ", Label.RIGHT));
+    tmp.add(colourPanel);
+
+    bigPanel.add(panel, BorderLayout.NORTH);
+
+    panel = new Panel();
+    panel.add(new Label("Description: ", Label.RIGHT));
+    panel.add(new ScrollPane().add(description));
+
+    if (!newFeatures)
+    {
+      bigPanel.add(panel, BorderLayout.SOUTH);
+
+      panel = new Panel();
+      panel.add(new Label(" Start:", Label.RIGHT));
+      panel.add(start);
+      panel.add(new Label("  End:", Label.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
       {
-        if(fstart<0) // fix for if the feature we have starts before the sequence start,
-          fstart = 0;// but the feature end is still valid!!
+        lastFeatureAdded = "feature_1";
+      }
+    }
 
-        if(fstart==fend)
+    if (lastFeatureGroupAdded == null)
+    {
+      if (features[0].featureGroup != null)
+      {
+        lastFeatureGroupAdded = features[0].featureGroup;
+      }
+      else
+      {
+        lastFeatureAdded = "Jalview";
+      }
+    }
+
+
+    String title = newFeatures ? "Create New Sequence Feature(s)" :
+        "Amend/Delete Features for "
+        + sequences[0].getName();
+
+    final JVDialog dialog = new JVDialog(ap.alignFrame,
+                               title,
+                               true,
+                               385,240);
+
+    dialog.setMainPanel(bigPanel);
+
+    if(newFeatures)
+    {
+      name.setText(lastFeatureAdded);
+      source.setText(lastFeatureGroupAdded);
+    }
+    else
+    {
+      dialog.ok.setLabel("Amend");
+      dialog.buttonPanel.add(deleteButton, 1);
+      deleteButton.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent evt)
+            {
+              deleteFeature = true;
+              dialog.setVisible(false);
+            }
+          });
+      name.setText(features[0].getType());
+      source.setText(features[0].getFeatureGroup());
+    }
+
+    start.setText(features[0].getBegin()+"");
+    end.setText(features[0].getEnd()+"");
+    description.setText(features[0].getDescription());
+
+    Color col = getColour(name.getText());
+    if (col == null)
+    {
+      col = new
+          jalview.schemes.UserColourScheme()
+          .createColourFromName(name.getText());
+    }
+
+    colourPanel.setBackground(col);
+
+    dialog.setResizable(true);
+
+
+    colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+    {
+      public void mousePressed(java.awt.event.MouseEvent evt)
+      {
+        new UserDefinedColours(fr, ap.alignFrame);
+      }
+    });
+
+    dialog.setVisible(true);
+
+    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+    if (dialog.accept)
+    {
+      //This ensures that the last sequence
+      //is refreshed and new features are rendered
+      lastSeq = null;
+      lastFeatureAdded = name.getText().trim();
+      lastFeatureGroupAdded = source.getText().trim();
+      lastDescriptionAdded = description.getText().replace('\n', ' ');
+    }
+
+    if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)
+      lastFeatureGroupAdded = null;
+
+
+    if (!newFeatures)
+    {
+      SequenceFeature sf = features[featureIndex];
+
+      if (dialog.accept)
+      {
+        sf.type = lastFeatureAdded;
+        sf.featureGroup = lastFeatureGroupAdded;
+        sf.description = lastDescriptionAdded;
+        setColour(sf.type, colourPanel.getBackground());
+        try
         {
-          g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
-          g.setColor(Color.white);
+          sf.begin = Integer.parseInt(start.getText());
+          sf.end =  Integer.parseInt(end.getText());
+        }
+        catch (NumberFormatException ex)
+        {}
 
-          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);
+        ffile.parseDescriptionHTML(sf, false);
+      }
+      if (deleteFeature)
+      {
+        sequences[0].deleteFeature(sf);
+      }
 
+    }
+    else
+    {
+      if (dialog.accept && name.getText().length()>0)
+      {
+        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);
         }
-        else
+
+        if (av.featuresDisplayed == null)
         {
-          for (int i = fstart; i <= fend; i++)
+          av.featuresDisplayed = new Hashtable();
+        }
+
+        if (featureGroups == null)
+        {
+          featureGroups = new Hashtable();
+        }
+
+        col = colourPanel.getBackground();
+        setColour(lastFeatureAdded, col);
+
+        if(lastFeatureGroupAdded!=null)
+        {
+          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+          av.featuresDisplayed.put(lastFeatureGroupAdded,
+                                   new Integer(col.getRGB()));
+        }
+        findAllFeatures();
+
+        String [] tro = new String[renderOrder.length];
+        tro[0] = renderOrder[renderOrder.length-1];
+        System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);
+        renderOrder = tro;
+
+        ap.paintAlignment(true);
+
+        return true;
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    findAllFeatures();
+
+    ap.paintAlignment(true);
+
+    return true;
+  }
+
+
+  public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+  {
+    overview = true;
+    if (!av.showSequenceFeatures)
+    {
+      return initialCol;
+    }
+
+    lastSeq = seq;
+    sequenceFeatures = lastSeq.getSequenceFeatures();
+    if (sequenceFeatures == null)
+    {
+      return initialCol;
+    }
+
+    sfSize = sequenceFeatures.length;
+
+    if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))
+    {
+      return Color.white;
+    }
+
+    currentColour = null;
+
+    drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);
+
+    if (currentColour == null)
+    {
+      return initialCol;
+    }
+
+    return new Color( ( (Integer) currentColour).intValue());
+  }
+
+  /**
+   * This is used by the Molecule Viewer to get the accurate colour
+   * of the rendered sequence
+   */
+  boolean overview = false;
+
+
+  /**
+   * 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;
+
+  synchronized public void drawSequence(Graphics g, SequenceI seq,
+                           int start, int end, int y1)
+  {
+    if (seq.getSequenceFeatures() == null
+        || seq.getSequenceFeatures().length == 0)
+    {
+      return;
+    }
+
+    if (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, transparency);
+    }
+
+    if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())
+    {
+      lastSeq = seq;
+      sequenceFeatures = seq.getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+
+    if (av.featuresDisplayed == null || renderOrder == null)
+    {
+      findAllFeatures();
+      if (av.featuresDisplayed.size() < 1)
+      {
+        return;
+      }
+
+      sequenceFeatures = seq.getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+    if (!overview)
+    {
+      spos = lastSeq.findPosition(start);
+      epos = lastSeq.findPosition(end);
+      if (g != null)
+      {
+        fm = g.getFontMetrics();
+      }
+    }
+    String type;
+    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+    {
+      type = renderOrder[renderIndex];
+      if (!av.featuresDisplayed.containsKey(type))
+      {
+        continue;
+      }
+
+      // loop through all features in sequence to find
+      // current feature to render
+      for (sfindex = 0; sfindex < sfSize; sfindex++)
+      {
+        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 (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+                          || sequenceFeatures[sfindex].getEnd() < spos))
+        {
+          continue;
+        }
+
+        if (overview)
+        {
+          if (sequenceFeatures[sfindex].begin <= start &&
+              sequenceFeatures[sfindex].end >= start)
           {
-            char s = seq.getSequence().charAt(i);
-            if( jalview.util.Comparison.isGap(s) )
-              continue;
+            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);
+        }
+
+      }
+    }
+
+    if (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, 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!!
+      }
 
-            g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
+      if (fend >= end)
+      {
+        fend = end;
+      }
+
+      for (i = fstart; i <= fend; i++)
+      {
+        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 (!av.validCharWidth)
+        {
+          continue;
+        }
+
+        g.setColor(Color.white);
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        g.drawString(String.valueOf(s),
+                     charOffset + (av.charWidth * (i - start)),
+                     (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+
+      }
+    }
+  }
 
-            g.setColor(Color.white);
+  void findAllFeatures()
+  {
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
+
+    av.featuresDisplayed = new Hashtable();
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceFeature[] features = av.alignment.getSequenceAt(i).
+          getSequenceFeatures();
 
-            FontMetrics fm = g.getFontMetrics();
-            int charOffset = (width - fm.charWidth(s)) / 2;
-            int pady = height / 5;
-            g.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i-start),
-                         y1 + height - pady);
+      if (features == null)
+      {
+        continue;
+      }
+
+      int index = 0;
+      while (index < features.length)
+      {
+        if (!av.featuresDisplayed.containsKey(features[index].getType()))
+        {
+          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--;
     }
-   }
+  }
 
+  public Color getColour(String featureType)
+  {
+    if (!featureColours.containsKey(featureType))
+    {
+      jalview.schemes.UserColourScheme ucs = new
+          jalview.schemes.UserColourScheme();
+      Color col = ucs.createColourFromName(featureType);
+      featureColours.put(featureType, col);
+      return col;
+    }
+    else
+      return (Color) featureColours.get(featureType);
+  }
+
+
+  public void setColour(String featureType, Color col)
+  {
+    featureColours.put(featureType, col);
+  }
+
+  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();
+    }
+
+   /* if (visibleNew)
+    {
+      if (av.featuresDisplayed != null)
+      {
+        av.featuresDisplayed.clear();
+      }
+      else
+      {
+        av.featuresDisplayed = new Hashtable();
+      }
+    }
+    if (data == null)
+    {
+      return;
+    }*/
+
+
+    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;
+      }
+    }
+  }
+}
+
+class TransparencySetter
+{
+  void setTransparency(Graphics g, float value)
+  {
+     Graphics2D g2 = (Graphics2D) g;
+     g2.setComposite(
+        AlphaComposite.getInstance(
+             AlphaComposite.SRC_OVER, value));
+  }
 }