X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=003200d754eedbd6406fc6797773305026754e36;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=591fa79acc6b1f05044d684a90a8608f329ccb18;hpb=50779cf7013a8db695c53637578ab135da3ce5b1;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 591fa79..003200d 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -25,6 +25,9 @@ import java.awt.*;
 import java.util.*;
 
 import java.awt.image.*;
+import javax.swing.*;
+import javax.swing.JOptionPane;
+import java.awt.event.*;
 
 
 /**
@@ -41,18 +44,19 @@ public class FeatureRenderer
     FontMetrics fm;
     int charOffset;
 
+    Hashtable featureColours = new Hashtable();
+
+
     // 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.
      *
@@ -61,7 +65,6 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)
     {
         this.av = av;
-        initColours();
     }
 
     public void transferSettings(FeatureRenderer fr)
@@ -76,33 +79,30 @@ public class FeatureRenderer
     boolean offscreenRender = false;
     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
     {
-      int seqindex = av.alignment.findIndex(seq);
-
       return new Color( findFeatureColour (initialCol.getRGB(),
-                        seqindex, res ));
+                        seq, res ));
     }
 
     /**
-     * This is used by the Molecule Viewer to get the accurate colour
-     * of the rendered sequence
+     * This is used by the Molecule Viewer and Overview to
+     * get the accurate colourof the rendered sequence
      */
-    public int findFeatureColour(int initialCol, int seqIndex, int column)
+    public int findFeatureColour(int initialCol, SequenceI seq, int column)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
 
-      if(seqIndex!=lastSequenceIndex)
+      if(seq!=lastSeq)
       {
-        lastSequence = av.alignment.getSequenceAt(seqIndex);
-        lastSequenceIndex = seqIndex;
-        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
+        lastSeq = seq;
+        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
         if(sequenceFeatures==null)
           return initialCol;
 
         sfSize = sequenceFeatures.length;
       }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
         return Color.white.getRGB();
 
 
@@ -120,7 +120,7 @@ public class FeatureRenderer
       {
         offscreenImage.setRGB(0,0,initialCol);
         drawSequence(offscreenImage.getGraphics(),
-                     lastSequence,
+                     lastSeq,
                      column,column,0);
 
         return offscreenImage.getRGB(0,0);
@@ -128,8 +128,8 @@ public class FeatureRenderer
       else
       {
         drawSequence(null,
-                    lastSequence,
-                    lastSequence.findPosition(column),
+                    lastSeq,
+                    lastSeq.findPosition(column),
                     -1, -1);
 
         if (currentColour == null)
@@ -157,8 +157,7 @@ public class FeatureRenderer
      */
    // String type;
    // SequenceFeature sf;
-    int lastSequenceIndex=-1;
-    SequenceI lastSequence;
+    SequenceI lastSeq;
     SequenceFeature [] sequenceFeatures;
     int sfSize, sfindex, spos, epos;
 
@@ -169,12 +168,13 @@ public class FeatureRenderer
           || seq.getDatasetSequence().getSequenceFeatures().length==0)
         return;
 
-
       if(g!=null)
         fm = g.getFontMetrics();
 
 
-      if (av.featuresDisplayed == null || renderOrder==null)
+      if (av.featuresDisplayed == null
+          || renderOrder==null
+          || newFeatureAdded)
        {
          findAllFeatures();
          if(av.featuresDisplayed.size()<1)
@@ -184,9 +184,9 @@ public class FeatureRenderer
          sfSize = sequenceFeatures.length;
        }
 
-       if(lastSequence==null || seq!=lastSequence)
+       if(lastSeq==null || seq!=lastSeq)
       {
-        lastSequence = seq;
+        lastSeq = seq;
         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
         sfSize = sequenceFeatures.length;
       }
@@ -202,8 +202,8 @@ public class FeatureRenderer
 
       if(!offscreenRender)
       {
-        spos = lastSequence.findPosition(start);
-        epos = lastSequence.findPosition(end);
+        spos = lastSeq.findPosition(start);
+        epos = lastSeq.findPosition(end);
       }
 
 
@@ -211,7 +211,8 @@ public class FeatureRenderer
       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
        {
         type =  renderOrder[renderIndex];
-        if(!av.featuresDisplayed.containsKey(type))
+
+        if(type==null || !av.featuresDisplayed.containsKey(type))
           continue;
 
         // loop through all features in sequence to find
@@ -308,7 +309,7 @@ public class FeatureRenderer
           int pady = (y1 + av.charHeight) - av.charHeight / 5;
           for (i = fstart; i <= fend; i++)
           {
-            s = seq.getSequence().charAt(i);
+            s = seq.getCharAt(i);
 
             if (jalview.util.Comparison.isGap(s))
             {
@@ -332,9 +333,34 @@ public class FeatureRenderer
       }
     }
 
-    synchronized void findAllFeatures()
+
+    boolean newFeatureAdded = false;
+
+    public void featuresAdded()
     {
-      av.featuresDisplayed = new Hashtable();
+      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++)
       {
@@ -355,7 +381,11 @@ public class FeatureRenderer
               // and we don't want to render the feature in the normal way
 
               if (getColour(features[index].getType()) == null)
-                createRandomColour(features[index].getType());
+              {
+                 featureColours.put(features[index].getType(),
+                                   ucs.createColourFromName(features[index].
+                    getType()));
+              }
 
               av.featuresDisplayed.put(features[index].getType(),
                                        new Integer(getColour(features[index].
@@ -375,6 +405,8 @@ public class FeatureRenderer
         renderOrder[i] = en.nextElement().toString();
         i--;
       }
+
+      findingFeatures = false;
     }
 
     public Color getColour(String featureType)
@@ -384,17 +416,270 @@ public class FeatureRenderer
     }
 
 
-    public void addNewFeature(String name, Color col, String group)
+    static String lastFeatureAdded;
+    static String lastFeatureGroupAdded;
+    static String lastDescriptionAdded;
+
+    public boolean createNewFeatures(SequenceI[] sequences,
+                                  SequenceFeature [] features)
     {
+      return amendFeatures(sequences, features, true, null);
+    }
 
-      setColour(name, col);
-      if(av.featuresDisplayed==null)
-        av.featuresDisplayed = new Hashtable();
+    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(group == null)
-        group = "NOGROUP";
+        if (getColour(lastFeatureAdded) != null)
+        {
+          colour.setBackground(getColour(lastFeatureAdded));
+        }
+        else
+        {
+          colour.setBackground(new Color(60, 160, 115));
+        }
 
-      av.featuresDisplayed.put(name, new Integer(col.getRGB()));
+      }
+      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)
@@ -439,59 +724,7 @@ public class FeatureRenderer
 
     }
 
-    Hashtable featureColours = new Hashtable();
-    void initColours()
-    {
-      featureColours.put("active site", new Color(255, 75, 0));
-      featureColours.put("binding site", new Color(245, 85, 0));
-      featureColours.put("calcium-binding region", new Color(235, 95, 0));
-      featureColours.put("chain", new Color(225, 105, 0));
-      featureColours.put("coiled-coil region", new Color(215, 115, 0));
-      featureColours.put("compositionally biased region", new Color(205, 125, 0));
-      featureColours.put("cross-link", new Color(195, 135, 0));
-      featureColours.put("disulfide bond", new Color(230,230,0));
-      featureColours.put("DNA-binding region", new Color(175, 155, 0));
-      featureColours.put("domain", new Color(165, 165, 0));
-      featureColours.put("glycosylation site", new Color(155, 175, 0));
-      featureColours.put("helix", new Color(145, 185, 0));
-      featureColours.put("initiator methionine", new Color(135, 195, 5));
-      featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));
-      featureColours.put("metal ion-binding site", new Color(115, 215, 25));
-      featureColours.put("modified residue", new Color(105, 225, 35));
-      featureColours.put("mutagenesis site", new Color(95, 235, 45));
-      featureColours.put("non-consecutive residues", new Color(85, 245, 55));
-      featureColours.put("non-terminal residue", new Color(75, 255, 65));
-      featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));
-      featureColours.put("peptide", new Color(55, 235, 85));
-      featureColours.put("propeptide", new Color(45, 225, 95));
-      featureColours.put("region of interest", new Color(35, 215, 105));
-      featureColours.put("repeat", new Color(25, 205, 115));
-      featureColours.put("selenocysteine", new Color(15, 195, 125));
-      featureColours.put("sequence conflict", new Color(5, 185, 135));
-      featureColours.put("sequence variant", new Color(0, 175, 145));
-      featureColours.put("short sequence motif", new Color(0, 165, 155));
-      featureColours.put("signal peptide", new Color(0, 155, 165));
-      featureColours.put("site", new Color(0, 145, 175));
-      featureColours.put("splice variant", new Color(0, 135, 185));
-      featureColours.put("strand", new Color(0, 125, 195));
-      featureColours.put("topological domain", new Color(0, 115, 205));
-      featureColours.put("transit peptide", new Color(0, 105, 215));
-      featureColours.put("transmembrane region", new Color(0, 95, 225));
-      featureColours.put("turn", new Color(0, 85, 235));
-      featureColours.put("unsure residue", new Color(0, 75, 245));
-      featureColours.put("zinc finger region", new Color(0, 65, 255));
-    }
 
-    public Color createRandomColour(String name)
-    {
-      Random rg = new Random(System.currentTimeMillis());
-      Color color = new Color( (int) (Math.random() * 255),
-                                         (int) (Math.random() * 255),
-                                         (int) (Math.random() * 255));
-      featureColours.put(name, color); // java 1.2 here ?
-
-      return color;
-    }
 
 
 }