Feature settings

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 57150c3..a4b7f06 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -57,8 +57,9 @@ public class OverviewPanel
     sr = new SequenceRenderer(av);\r
     sr.graphics = nullFrame.getGraphics();\r
     sr.renderGaps( false );\r
+    sr.forOverview = true;\r
     fr = new FeatureRenderer(av);\r
-    fr.drawText = false;\r
+    fr.overview = true;\r
 \r
 \r
 \r
@@ -184,8 +185,10 @@ public class OverviewPanel
     }\r
 \r
     if (av.showSequenceFeatures)\r
-      fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
-\r
+   {\r
+     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
+     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+   }\r
 \r
     resizing = true;\r
 \r
@@ -212,6 +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
@@ -232,50 +243,78 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;\r
     float sampleRow = (float) alheight / (float) sequencesHeight;\r
 \r
-    int lastcol=-1, lastrow=-1;\r
+    int lastcol=0, lastseq=0;\r
+    int xstart=0, ystart=0;\r
     Color color = Color.yellow;\r
-    int row, col;\r
-    for (col = 0; col < width; col++)\r
+    int col, sameRow = 0, sameCol = 0;\r
+    jalview.datamodel.SequenceI sequence;\r
+\r
+    for (int row = 0; row <= sequencesHeight; row++)\r
     {\r
-      for (row = 0; row < sequencesHeight; row++)\r
+      if((int)(row*sampleRow)==lastseq)\r
       {\r
-        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
-        {\r
-          mg.drawLine(col, row, col, row);\r
-          continue;\r
-        }\r
+        sameRow ++;\r
+        continue;\r
+      }\r
 \r
-        if (av.conservation != null)\r
+      sequence = av.getAlignment().getSequenceAt(lastseq);\r
+\r
+      for (col = 0; col < width; col++)\r
+      {\r
+        if((int)(col*sampleCol) == lastcol)\r
         {\r
-          mg.translate(col, sequencesHeight);\r
-          ap.annotationPanel.drawGraph(mg, av.conservation,\r
-                                       (int) (sampleCol) + 1,\r
-                                       graphHeight,\r
-                                       (int) (col * sampleCol),\r
-                                       (int) (col * sampleCol) + 1);\r
-          mg.translate( -col, -sequencesHeight);\r
+          sameCol ++;\r
+          continue;\r
         }\r
 \r
-        lastrow = (int)(row*sampleRow);\r
         lastcol = (int)(col*sampleCol);\r
 \r
-        if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
+        if(sequence.getLength()>lastcol)\r
         {\r
-          color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
-\r
+          color = sr.findSequenceColour(sequence, lastcol);\r
 \r
           if (av.showSequenceFeatures)\r
             color = fr.findFeatureColour(color,\r
-                                        av.alignment.getSequenceAt(lastrow),\r
-                                         lastcol);\r
+                                        sequence,\r
+                                        lastcol);\r
         }\r
+        else\r
+          color = color.white;\r
 \r
         mg.setColor(color);\r
-        mg.drawLine(col,row,col,row);\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
+    {\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
+                                       (int) (sampleCol) + 1,\r
+                                       graphHeight,\r
+                                       (int) (col * sampleCol),\r
+                                       (int) (col * sampleCol) + 1);\r
+          mg.translate( -col, -sequencesHeight);\r
+        }\r
+      }\r
+    }\r
+\r
+\r
 \r
     System.gc();\r
 \r