Overview subsamples alignment

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 3cd229d..7910f2d 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -32,11 +32,16 @@ public class OverviewPanel
   float scaleh = 1f;\r
 \r
   public int width, sequencesHeight;\r
-  int graphHeight = 30;\r
+  int graphHeight = 20;\r
   int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;\r
 \r
   boolean resizing = false;\r
 \r
+  // Can set different properties in this seqCanvas than\r
+  // main visible SeqCanvas\r
+  SeqCanvas overviewSeq;\r
+\r
+\r
   Frame nullFrame;\r
 \r
   public OverviewPanel(AlignmentPanel ap)\r
@@ -47,14 +52,25 @@ public class OverviewPanel
     nullFrame = new Frame();\r
     nullFrame.addNotify();\r
 \r
+    overviewSeq = new SeqCanvas(av);\r
+    overviewSeq.isOverview = true;\r
+    overviewSeq.sr.renderGaps = false;\r
+\r
+\r
     // scale the initial size of overviewpanel to shape of alignment\r
     float initialScale = (float) av.alignment.getWidth() /\r
         (float) av.alignment.getHeight();\r
+\r
+    if(av.vconsensus==null)\r
+          graphHeight = 0;\r
+\r
     if (av.alignment.getWidth() > av.alignment.getHeight())\r
     {\r
       // wider\r
       width = 400;\r
       sequencesHeight = (int) (400f / initialScale);\r
+      if(sequencesHeight<40)\r
+              sequencesHeight = 40;\r
     }\r
     else\r
     {\r
@@ -212,83 +228,36 @@ public class OverviewPanel
     miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);\r
 \r
     Graphics mg = miniMe.getGraphics();\r
-    Image consensus = nullFrame.createImage(fullsizeWidth, 60);\r
-    Graphics g = consensus.getGraphics();\r
-    ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
-    mg.drawImage(consensus, 0, sequencesHeight, width,\r
-                 sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
-\r
-    boolean oldRenderGaps = av.renderGaps;\r
-    try\r
-    {\r
-      // We'll have to draw the full size alignment in chunks, as an image of the\r
-      // whole alignment requires too much memory\r
+    float sampleCol = (float) alwidth / (float) width;\r
+    float sampleRow = (float) alheight / (float) sequencesHeight;\r
 \r
-      // Max size depends on the font size, the following is a\r
-      // guess at a size which works\r
-      int maxSize = 2000 / av.getFont().getSize();\r
-      Image block;\r
-      int blockx = 0, blocky = 0, blockw = 0, blockh = 0, eRes = 0, eSeq = 0;\r
-\r
-      av.setRenderGaps(false);\r
-      for (int sRes = 0, chunkx = 0; sRes < alwidth; sRes += maxSize, chunkx++)\r
+    for (int col = 0; col < width; col++)\r
+    {\r
+      for (int row = 0; row < sequencesHeight; row++)\r
       {\r
-        eSeq = 0;\r
-        eRes += maxSize;\r
-        if (eRes > alwidth)\r
-        {\r
-          eRes = alwidth;\r
-        }\r
-\r
-        for (int sSeq = 0, chunky = 0; sSeq < alheight; sSeq += maxSize, chunky++)\r
-        {\r
-          if(resizeAgain)\r
-                  break;\r
-\r
-          eSeq += maxSize;\r
-          if (eSeq > alheight)\r
-          {\r
-            eSeq = alheight;\r
-          }\r
-\r
-          blocky = 0;\r
-          blockx = (int) ( (float) sRes / (float) alwidth * width);\r
-\r
-          block = nullFrame.createImage( (eRes - sRes) * av.charWidth,\r
-                                        (eSeq - sSeq) * av.charHeight);\r
-          g = block.getGraphics();\r
-\r
-          ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq,\r
-                                          0);\r
-\r
-          blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *\r
-                          sequencesHeight) + 1;\r
-          blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) + 1;\r
-\r
-          blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);\r
-\r
-          mg.drawImage(block, blockx,\r
-                       blocky,\r
-                       blockx + blockw,\r
-                       blocky + blockh,\r
-\r
-                       0, 0, block.getWidth(null), block.getHeight(null), this);\r
-\r
-          block = null;\r
-        }\r
+        overviewSeq.drawPanel(mg,\r
+                                        (int) (col * sampleCol),\r
+                                        (int) (col * sampleCol),\r
+                                        (int) (row * sampleRow),\r
+                                        (int) (row * sampleRow) + 1,\r
+                                        (int) (col * sampleCol),\r
+                                        (int) (row * sampleRow), 0);\r
+        mg.translate(0, 1);\r
+\r
+        if (av.conservation != null)\r
+          ap.annotationPanel.drawGraph(mg, av.conservation,\r
+                                       (int) (sampleCol) + 1,\r
+                                       graphHeight,\r
+                                       (int) (col * sampleCol),\r
+                                       (int) (col * sampleCol) + 1);\r
 \r
       }\r
+      mg.translate(0, -sequencesHeight);\r
+      mg.translate(1, 0);\r
 \r
-    }\r
-    catch (OutOfMemoryError error)\r
-    {\r
-      System.err.println(\r
-          "Out of memory when trying to calculate the overview window image!");\r
-    }\r
-\r
+        }\r
     System.gc();\r
 \r
-    av.setRenderGaps(oldRenderGaps);\r
     resizing = false;\r
 \r
     setBoxPosition();\r