Display only selected features

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index f315df6..372ecd7 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -68,31 +68,74 @@ public class FeatureRenderer
      * @param width DOCUMENT ME!\r
      * @param height DOCUMENT ME!\r
      */\r
-    public void drawSequence(Graphics g1, SequenceI seq, SequenceGroup[] sg,\r
-        int start, int end, int x1, int y1, int width, int height)\r
+    public void drawSequence(Graphics g, SequenceI seq,\r
+                             int start, int end, int x1, int y1, int width, int height)\r
     {\r
 \r
-        if(seq.getSequenceFeatures()==null)\r
-          return;\r
+      if (seq.getDatasetSequence().getSequenceFeatures() == null)\r
+        return;\r
 \r
-        Enumeration e = null, e2;\r
-        String type;\r
-        if(featuresDisplayed!=null)\r
-          e = featuresDisplayed.elements();\r
-        else\r
-         e = seq.getSequenceFeatures().elements();\r
-\r
-        Graphics2D g = (Graphics2D)g1;\r
-        g.setComposite(\r
-        AlphaComposite.getInstance(\r
-               AlphaComposite.SRC_OVER,transparency));\r
+      if (transparency != 1)\r
+      {\r
+        Graphics2D g2 = (Graphics2D) g;\r
+        g2.setComposite(\r
+            AlphaComposite.getInstance(\r
+                AlphaComposite.SRC_OVER, transparency));\r
+      }\r
 \r
+      Enumeration e, e2;\r
+      String type;\r
+      SequenceFeature sf;\r
+      if (featuresDisplayed != null)\r
+      {\r
+           e = featuresDisplayed.elements();\r
+           while(e.hasMoreElements())\r
+           {\r
+             type = e.nextElement().toString();\r
+             e2 = seq.getDatasetSequence().getSequenceFeatures().elements();\r
+             while(e2.hasMoreElements())\r
+             {\r
+               sf = (SequenceFeature) e2.nextElement();\r
+               if(!type.equals(sf.getType() ) )\r
+                  continue;\r
+\r
+               if (sf.getBegin() > seq.getEnd())\r
+                  continue;\r
+\r
+               renderFeature(g,seq,\r
+                         seq.findIndex(sf.getBegin()) - 1,\r
+                         seq.findIndex(sf.getEnd()) - 1,\r
+                         type,start,end,x1,y1,width,height);\r
+             }\r
+           }\r
+      }\r
+      else\r
+      {\r
+        e = seq.getDatasetSequence().getSequenceFeatures().elements();\r
         while (e.hasMoreElements())\r
         {\r
+          sf = (SequenceFeature) e.nextElement();\r
+          type = sf.getType();\r
+\r
+          if (sf.getBegin() > seq.getEnd())\r
+          {\r
+            continue;\r
+          }\r
+\r
+          renderFeature(g,seq,\r
+                        seq.findIndex(sf.getBegin()) - 1,\r
+                        seq.findIndex(sf.getEnd()) - 1,\r
+                        type,start,end,x1,y1,width,height);\r
+\r
+        }\r
+      }\r
+\r
+   /*       while (e.hasMoreElements())\r
+        {\r
             SequenceFeature sf=null;\r
             if(featuresDisplayed!=null)\r
             {\r
-              e2 = seq.getSequenceFeatures().elements();\r
+              e2 = seq.getDatasetSequence().getSequenceFeatures().elements();\r
               type = e.nextElement().toString();\r
               while(e2.hasMoreElements())\r
               {\r
@@ -120,64 +163,72 @@ public class FeatureRenderer
 \r
             int fstart = seq.findIndex(sf.getBegin()) - 1;\r
             int fend = seq.findIndex(sf.getEnd()) - 1;\r
+*/\r
 \r
-            if (((fstart <= end) && (fend >= start)))\r
-            {\r
-                if (fstart < start)\r
-                { // fix for if the feature we have starts before the sequence start,\r
-                    fstart = start; // but the feature end is still valid!!\r
-                }\r
-\r
-                if (fend >= end)\r
-                {\r
-                    fend = end;\r
-                }\r
-\r
-                if (fstart == fend)\r
-                {\r
-                    g.setColor(getColour(type));\r
-                    g.fillRoundRect((fstart - start) * width, y1, width,\r
-                        height, 4, 4);\r
-                    g.setColor(Color.white);\r
-\r
-                    char s = seq.getSequence().charAt(fstart);\r
-                    FontMetrics fm = g.getFontMetrics();\r
-                    int charOffset = (width - fm.charWidth(s)) / 2;\r
-                    int pady = height / 5;\r
-                    g.drawString(String.valueOf(s),\r
-                        charOffset + x1 + (width * (fstart - start)),\r
-                        (y1 + height) - pady);\r
-                }\r
-                else\r
-                {\r
-                    for (int i = fstart; i <= fend; i++)\r
-                    {\r
-                        char s = seq.getSequence().charAt(i);\r
-\r
-                        if (jalview.util.Comparison.isGap(s))\r
-                        {\r
-                            continue;\r
-                        }\r
-\r
-                        g.setColor(getColour(type));\r
-                        g.fillRect((i - start) * width, y1, width, height);\r
-\r
-                        g.setColor(Color.white);\r
-\r
-                        FontMetrics fm = g.getFontMetrics();\r
-                        int charOffset = (width - fm.charWidth(s)) / 2;\r
-                        int pady = height / 5;\r
-                        g.drawString(String.valueOf(s),\r
-                            charOffset + x1 + (width * (i - start)),\r
-                            (y1 + height) - pady);\r
-                    }\r
-                }\r
-            }\r
+        if(transparency!=1.0f)\r
+        {\r
+          Graphics2D g2 = (Graphics2D) g;\r
+          g2.setComposite(\r
+              AlphaComposite.getInstance(\r
+                  AlphaComposite.SRC_OVER, 1.0f));\r
         }\r
-        g.setComposite(\r
-        AlphaComposite.getInstance(\r
-               AlphaComposite.SRC_OVER,1.0f));\r
+    }\r
 \r
+    void renderFeature(Graphics g, SequenceI seq,\r
+                       int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)\r
+    {\r
+      if (((fstart <= end) && (fend >= start)))\r
+      {\r
+          if (fstart < start)\r
+          { // fix for if the feature we have starts before the sequence start,\r
+              fstart = start; // but the feature end is still valid!!\r
+          }\r
+\r
+          if (fend >= end)\r
+          {\r
+              fend = end;\r
+          }\r
+\r
+          if (fstart == fend)\r
+          {\r
+              g.setColor(getColour(type));\r
+              g.fillRoundRect((fstart - start) * width, y1, width,\r
+                  height, 4, 4);\r
+              g.setColor(Color.white);\r
+\r
+              char s = seq.getSequence().charAt(fstart);\r
+              FontMetrics fm = g.getFontMetrics();\r
+              int charOffset = (width - fm.charWidth(s)) / 2;\r
+              int pady = height / 5;\r
+              g.drawString(String.valueOf(s),\r
+                  charOffset + x1 + (width * (fstart - start)),\r
+                  (y1 + height) - pady);\r
+          }\r
+          else\r
+          {\r
+              for (int i = fstart; i <= fend; i++)\r
+              {\r
+                  char s = seq.getSequence().charAt(i);\r
+\r
+                  if (jalview.util.Comparison.isGap(s))\r
+                  {\r
+                      continue;\r
+                  }\r
+\r
+                  g.setColor(getColour(type));\r
+                  g.fillRect((i - start) * width, y1, width, height);\r
+\r
+                  g.setColor(Color.white);\r
+\r
+                  FontMetrics fm = g.getFontMetrics();\r
+                  int charOffset = (width - fm.charWidth(s)) / 2;\r
+                  int pady = height / 5;\r
+                  g.drawString(String.valueOf(s),\r
+                      charOffset + x1 + (width * (i - start)),\r
+                      (y1 + height) - pady);\r
+              }\r
+          }\r
+      }\r
     }\r
 \r
     public Color getColour(String featureType)\r

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index fd413e0..28cb295 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -8,7 +8,6 @@ import java.util.*;
 import javax.swing.BorderFactory;\r
 import java.awt.event.*;\r
 import javax.swing.table.*;\r
-import java.io.*;\r
 \r
 public class FeatureSettings extends JPanel\r
 {\r
@@ -24,7 +23,7 @@ public class FeatureSettings extends JPanel
     av.alignment.getSequences();\r
     final JInternalFrame frame = new JInternalFrame();\r
     frame.setContentPane(this);\r
-    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 500, 300);\r
+    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);\r
 \r
 \r
     Vector allFeatures = new Vector();\r
@@ -32,10 +31,9 @@ public class FeatureSettings extends JPanel
     Enumeration e;\r
     SequenceFeature sf;\r
 \r
-\r
     for(int i=0; i< av.alignment.getHeight(); i++)\r
     {\r
-       features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
+       features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
        if(features==null)\r
          continue;\r
 \r
@@ -68,10 +66,18 @@ public class FeatureSettings extends JPanel
       Color col = fr.getColour(type);\r
       data[i][0]=type;\r
       data[i][1]=col;\r
-      data[i][2]= new Boolean(true);\r
+      if(fr.featuresDisplayed!=null)\r
+         data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
+      else\r
+        data[i][2] = new Boolean(true);\r
+\r
       originalData[i][0]=type;\r
       originalData[i][1]=col;\r
-      originalData[i][2]= new Boolean(true);\r
+      if(fr.featuresDisplayed!=null)\r
+         originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
+      else\r
+        originalData[i][2] = new Boolean(true);\r
+\r
     }\r
 \r
     final JSlider transparency = new JSlider(0,70,0);\r
@@ -102,6 +108,8 @@ public class FeatureSettings extends JPanel
     table.setDefaultEditor(Color.class,\r
                       new ColorEditor());\r
 \r
+    table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
+\r
     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
 \r
     table.addMouseListener(new MouseAdapter()\r