Overview subsamples alignment

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 9e8f895..fd83309 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -43,6 +43,8 @@ public class SeqCanvas
 \r
   boolean fastPaint = false;\r
 \r
+  boolean isOverview = false;\r
+\r
   public SeqCanvas(AlignViewport av)\r
   {\r
     this.av = av;\r
@@ -203,6 +205,8 @@ public class SeqCanvas
 \r
   public void paint(Graphics g)\r
   {\r
+    sr.renderGaps(av.renderGaps);\r
+\r
     if (fastPaint)\r
     {\r
       g.drawImage(img, 0, 0, this);\r
@@ -408,7 +412,7 @@ public class SeqCanvas
       groupIndex = 0;\r
     }\r
 \r
-    if (group != null)\r
+    if (group != null && !isOverview)\r
     {\r
       do\r
       {\r

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c80a830..7086a51 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -40,13 +40,17 @@ public class OverviewPanel extends JPanel implements Runnable
     float scaleh = 1f;\r
     int width;\r
     int sequencesHeight;\r
-    int graphHeight = 30;\r
+    int graphHeight = 20;\r
     int boxX = -1;\r
     int boxY = -1;\r
     int boxWidth = -1;\r
     int boxHeight = -1;\r
     boolean resizing = false;\r
 \r
+    // Can set different properties in this seqCanvas than\r
+    // main visible SeqCanvas\r
+    SeqCanvas overviewSeq;\r
+\r
     /**\r
      * Creates a new OverviewPanel object.\r
      *\r
@@ -58,14 +62,24 @@ public class OverviewPanel extends JPanel implements Runnable
         this.ap = ap;\r
         setLayout(null);\r
 \r
+        overviewSeq = new SeqCanvas(av);\r
+        overviewSeq.isOverview = true;\r
+        overviewSeq.sr.renderGaps = false;\r
+\r
         // scale the initial size of overviewpanel to shape of alignment\r
         float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();\r
 \r
+        if(av.vconsensus==null)\r
+          graphHeight = 0;\r
+\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
@@ -204,6 +218,7 @@ public class OverviewPanel extends JPanel implements Runnable
           width = getWidth();\r
           sequencesHeight = getHeight() - graphHeight;\r
         }\r
+\r
         setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
         setBoxPosition();\r
 \r
@@ -238,117 +253,39 @@ public class OverviewPanel extends JPanel implements Runnable
                 BufferedImage.TYPE_INT_RGB);\r
 \r
 \r
-\r
         Graphics mg = miniMe.getGraphics();\r
-        BufferedImage consensus;\r
-        Graphics cg;\r
-        Graphics g ;\r
-\r
-        mg.setColor(Color.white);\r
-        mg.fillRect(0, 0, getWidth(), getHeight());\r
-        mg.setColor(Color.black);\r
-        mg.setFont(new Font("Verdana", Font.BOLD, 15));\r
-        mg.drawString("Recalculating", 5, sequencesHeight / 2);\r
-        mg.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);\r
 \r
-        boolean oldRenderGaps = av.renderGaps;\r
+        float sampleCol = (float) alwidth / (float) width;\r
+        float sampleRow = (float) alheight / (float) sequencesHeight;\r
 \r
-        try\r
+        for (int col = 0; col < width; col++)\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
-            // 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
-            BufferedImage block;\r
-            int blockx = 0;\r
-            int blocky = 0;\r
-            int blockw = 0;\r
-            int blockh = 0;\r
-            int eRes = 0;\r
-            int eSeq = 0;\r
-\r
-            av.setRenderGaps(false);\r
-\r
-            for (int sRes = 0, chunkx = 0; sRes < alwidth;\r
-                    sRes += maxSize, chunkx++)\r
-            {\r
-                if(resizeAgain)\r
-                  break;\r
-\r
-                eSeq = 0;\r
-                eRes += maxSize;\r
-\r
-                if (eRes > alwidth)\r
-                {\r
-                    eRes = alwidth;\r
-                }\r
-\r
-                for (int sSeq = 0, chunky = 0; sSeq < alheight;\r
-                        sSeq += maxSize, chunky++)\r
-                {\r
-                  if (resizeAgain)\r
-                    break;\r
-                    eSeq += maxSize;\r
-\r
-                    if (eSeq > alheight)\r
-                    {\r
-                        eSeq = alheight;\r
-                    }\r
-\r
-                    blocky = 0;\r
-                    blockx = (int) ((float) sRes / (float) alwidth * width);\r
+          for (int row = 0; row < sequencesHeight; row++)\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
-                    block = new BufferedImage((eRes - sRes) * av.charWidth,\r
-                            (eSeq - sSeq) * av.charHeight,\r
-                            BufferedImage.TYPE_3BYTE_BGR);\r
-                    g = block.getGraphics();\r
-\r
-                    ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,\r
-                        sRes, sSeq, 0);\r
-\r
-                    blockh = (int) ((float) (eSeq - sSeq) / (float) alheight * sequencesHeight) +\r
-                        1;\r
-                    blockw = (int) ((float) (eRes - sRes) / (float) alwidth * width) +\r
-                        1;\r
-\r
-                    blocky += (int) ((float) sSeq / (float) alheight * sequencesHeight);\r
-\r
-                    if(av.conservation!=null)\r
-                    {\r
-                      consensus = new BufferedImage( (eRes - sRes) * av.charWidth, 60,\r
-                                                    BufferedImage.TYPE_3BYTE_BGR);\r
-                      cg = consensus.getGraphics();\r
-\r
-                      ap.annotationPanel.drawGraph(cg, av.conservation,\r
-                                                   (eRes - sRes) * av.charWidth, 60, sRes, eRes);\r
-\r
-                      mg.drawImage(consensus, blockx, sequencesHeight, blockx + blockw,\r
-\r
-                                   sequencesHeight + graphHeight, 0, 0,\r
-                                   (eRes - sRes) * av.charWidth, 60, this);\r
-                    }\r
-\r
-                    mg.drawImage(block, blockx, blocky, blockx + blockw,\r
-                        blocky + blockh, 0, 0, block.getWidth(),\r
-                        block.getHeight(), null);\r
-\r
-                    block = null;\r
-                    repaint();\r
-                }\r
-\r
-\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
         System.gc();\r
 \r
-        av.setRenderGaps(oldRenderGaps);\r
         resizing = false;\r
 \r
         setBoxPosition();\r
@@ -386,7 +323,7 @@ public class OverviewPanel extends JPanel implements Runnable
      */\r
     public void paintComponent(Graphics g)\r
     {\r
-        if (miniMe != null)\r
+        if (miniMe != null && !resizing)\r
         {\r
           g.drawImage(miniMe, 0, 0, this);\r
         }\r
@@ -400,6 +337,7 @@ public class OverviewPanel extends JPanel implements Runnable
           g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);\r
         }\r
 \r
+\r
         g.setColor(Color.red);\r
         g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
         g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 9f1eb70..3cf7f9a 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -49,6 +49,8 @@ public class SeqCanvas extends JComponent
     int LABEL_WEST;\r
     int LABEL_EAST;\r
 \r
+    boolean isOverview = false;\r
+\r
     /**\r
      * Creates a new SeqCanvas object.\r
      *\r
@@ -254,6 +256,8 @@ public class SeqCanvas extends JComponent
     // Set this to false to force a full panel paint\r
     public void paintComponent(Graphics g)\r
     {\r
+        sr.renderGaps(av.renderGaps);\r
+\r
         if ((img != null) &&\r
                 (fastPaint || (getWidth() != g.getClipBounds().width) ||\r
                 (getHeight() != g.getClipBounds().height)))\r
@@ -276,11 +280,12 @@ public class SeqCanvas extends JComponent
             return;\r
         }\r
 \r
+\r
         img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
         gg = (Graphics2D) img.getGraphics();\r
         gg.setFont(av.getFont());\r
-     //   gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
-     //     RenderingHints.VALUE_ANTIALIAS_ON);\r
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+          RenderingHints.VALUE_ANTIALIAS_ON);\r
 \r
         gg.setColor(Color.white);\r
         gg.fillRect(0, 0, imgWidth, imgHeight);\r
@@ -453,7 +458,6 @@ public class SeqCanvas extends JComponent
     {\r
         Graphics2D g = (Graphics2D) g1;\r
         g.setFont(av.getFont());\r
-        sr.renderGaps(av.renderGaps);\r
 \r
         SequenceI nextSeq;\r
 \r
@@ -497,7 +501,7 @@ public class SeqCanvas extends JComponent
         }\r
 \r
 \r
-        if (group != null)\r
+        if (group != null && !isOverview)\r
         {\r
             do\r
             {\r