Feature settings

[jalview.git] / src / jalview / appletgui / OverviewPanel.java

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 23bfd09..a4b7f06 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -23,7 +23,7 @@ import java.awt.*;
 import java.awt.event.*;\r
 \r
 public class OverviewPanel\r
-    extends Panel implements Runnable\r
+    extends Panel implements Runnable, MouseMotionListener, MouseListener\r
 {\r
   Image miniMe;\r
   AlignViewport av;\r
@@ -40,7 +40,7 @@ public class OverviewPanel
   // Can set different properties in this seqCanvas than\r
   // main visible SeqCanvas\r
   SequenceRenderer sr;\r
-  //FeatureRenderer fr;\r
+  FeatureRenderer fr;\r
 \r
 \r
   Frame nullFrame;\r
@@ -57,9 +57,9 @@ public class OverviewPanel
     sr = new SequenceRenderer(av);\r
     sr.graphics = nullFrame.getGraphics();\r
     sr.renderGaps( false );\r
-    //fr = new FeatureRenderer(av);\r
-    //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
-    //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
+    sr.forOverview = true;\r
+    fr = new FeatureRenderer(av);\r
+    fr.overview = true;\r
 \r
 \r
 \r
@@ -103,32 +103,24 @@ public class OverviewPanel
       }\r
     });\r
 \r
-    addMouseMotionListener(new MouseMotionAdapter()\r
-    {\r
-      public void mouseDragged(MouseEvent evt)\r
-      {\r
-        doMouseDragged(evt);\r
-      }\r
-    });\r
+    addMouseMotionListener(this);\r
 \r
-    addMouseListener(new MouseAdapter()\r
-    {\r
-      public void mousePressed(MouseEvent evt)\r
-      {\r
-        doMousePressed(evt);\r
-      }\r
-\r
-      public void mouseReleased(MouseEvent evt)\r
-      {\r
-        doMouseReleased(evt);\r
-      }\r
-    });\r
+    addMouseListener(this);\r
 \r
     updateOverviewImage();\r
 \r
   }\r
 \r
-  public void doMousePressed(MouseEvent evt)\r
+\r
+  public void mouseEntered(MouseEvent evt)\r
+  {}\r
+  public void mouseExited(MouseEvent evt)\r
+  {}\r
+  public void mouseClicked(MouseEvent evt)\r
+  {}\r
+  public void mouseMoved(MouseEvent evt)\r
+  {}\r
+  public void mousePressed(MouseEvent evt)\r
   {\r
     boxX = evt.getX();\r
     boxY = evt.getY();\r
@@ -137,7 +129,7 @@ public class OverviewPanel
     repaint();\r
   }\r
 \r
-  public void doMouseReleased(MouseEvent evt)\r
+  public void mouseReleased(MouseEvent evt)\r
   {\r
     boxX = evt.getX();\r
     boxY = evt.getY();\r
@@ -146,7 +138,7 @@ public class OverviewPanel
                          (int) (boxY / scaleh / av.getCharHeight()));\r
   }\r
 \r
-  public void doMouseDragged(MouseEvent evt)\r
+  public void mouseDragged(MouseEvent evt)\r
   {\r
     boxX = evt.getX();\r
     boxY = evt.getY();\r
@@ -192,6 +184,12 @@ public class OverviewPanel
         return;\r
     }\r
 \r
+    if (av.showSequenceFeatures)\r
+   {\r
+     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
+     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+   }\r
+\r
     resizing = true;\r
 \r
     if ( (getSize().width > 0) && (getSize().height > 0))\r
@@ -217,6 +215,14 @@ public class OverviewPanel
     int alwidth = av.alignment.getWidth();\r
     int alheight = av.alignment.getHeight();\r
 \r
+    if (av.showSequenceFeatures)\r
+    {\r
+      fr.renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+      fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;\r
+    }\r
+\r
     if (getSize().width > 0 && getSize().height > 0)\r
     {\r
       width = getSize().width;\r
@@ -237,28 +243,65 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;\r
     float sampleRow = (float) alheight / (float) sequencesHeight;\r
 \r
-    int lastcol=-1, lastrow=-1;\r
-    Color color = Color.white;\r
-    for (int col = 0; col < width; col++)\r
+    int lastcol=0, lastseq=0;\r
+    int xstart=0, ystart=0;\r
+    Color color = Color.yellow;\r
+    int col, sameRow = 0, sameCol = 0;\r
+    jalview.datamodel.SequenceI sequence;\r
+\r
+    for (int row = 0; row <= sequencesHeight; row++)\r
     {\r
-      for (int row = 0; row < sequencesHeight; row++)\r
+      if((int)(row*sampleRow)==lastseq)\r
       {\r
-        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
+        sameRow ++;\r
+        continue;\r
+      }\r
+\r
+      sequence = av.getAlignment().getSequenceAt(lastseq);\r
+\r
+      for (col = 0; col < width; col++)\r
+      {\r
+        if((int)(col*sampleCol) == lastcol)\r
         {\r
-          mg.setColor(color);\r
-          mg.fillRect(col,row,1,1);\r
+          sameCol ++;\r
           continue;\r
         }\r
 \r
-        lastrow = (int)(row*sampleRow);\r
         lastcol = (int)(col*sampleCol);\r
 \r
-        color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
+        if(sequence.getLength()>lastcol)\r
+        {\r
+          color = sr.findSequenceColour(sequence, lastcol);\r
+\r
+          if (av.showSequenceFeatures)\r
+            color = fr.findFeatureColour(color,\r
+                                        sequence,\r
+                                        lastcol);\r
+        }\r
+        else\r
+          color = color.white;\r
 \r
         mg.setColor(color);\r
-        mg.fillRect(col,row,1,1);\r
+        if (sameCol == 1 && sameRow == 1)\r
+          mg.drawLine(xstart, ystart, xstart, ystart);\r
+        else\r
+          mg.fillRect(xstart, ystart, sameCol, sameRow);\r
+\r
+        xstart = col;\r
+        sameCol = 1;\r
+      }\r
+\r
+\r
+      lastseq = (int)(row*sampleRow);\r
+      ystart = row;\r
+      sameRow = 1;\r
+    }\r
 \r
-        if (av.conservation != null)\r
+    if (av.conservation != null)\r
+    {\r
+      for (col = 0; col < width; col++)\r
+      {\r
+        lastcol = (int) (col * sampleCol);\r
         {\r
           mg.translate(col, sequencesHeight);\r
           ap.annotationPanel.drawGraph(mg, av.conservation,\r
@@ -266,11 +309,13 @@ public class OverviewPanel
                                        graphHeight,\r
                                        (int) (col * sampleCol),\r
                                        (int) (col * sampleCol) + 1);\r
-          mg.translate(-col, -sequencesHeight);\r
+          mg.translate( -col, -sequencesHeight);\r
         }\r
       }\r
     }\r
 \r
+\r
+\r
     System.gc();\r
 \r
     resizing = false;\r