Wrap alignment with annotations

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f6e6114..8f5c74c 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -47,7 +47,7 @@ import javax.swing.*;
 public class AlignmentPanel extends GAlignmentPanel\r
     implements AdjustmentListener, Printable\r
 {\r
-    AlignViewport av;\r
+    public AlignViewport av;\r
     OverviewPanel overviewPanel;\r
     SeqPanel seqPanel;\r
     IdPanel idPanel;\r
@@ -134,6 +134,7 @@ public class AlignmentPanel extends GAlignmentPanel
             });\r
     }\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      */\r
@@ -625,7 +626,7 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
         if (av.showAnnotation)\r
         {\r
-            pagesHigh += annotationPanel.getHeight();\r
+            pagesHigh += annotationPanel.adjustPanelHeight()+3;\r
         }\r
 \r
         pagesHigh /= pheight;\r
@@ -685,7 +686,7 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
         if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
         {\r
-            pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);\r
+            pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight +3);\r
             alabels.drawComponent((Graphics2D) pg);\r
             pg.translate(idWidth, 0);\r
             annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +\r
@@ -710,17 +711,32 @@ public class AlignmentPanel extends GAlignmentPanel
     public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
         int pi) throws PrinterException\r
     {\r
-        int idWidth = calculateIdWidth().width + 4;\r
+\r
+      int annotationHeight = 0;\r
+      if (av.showAnnotation)\r
+        annotationHeight = annotationPanel.adjustPanelHeight();\r
+\r
+      int hgap = av.charHeight;\r
+      if (av.scaleAboveWrapped)\r
+        hgap += av.charHeight;\r
+\r
+      int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+          + hgap\r
+          + annotationHeight;\r
+\r
+\r
+      int idWidth = calculateIdWidth().width + 4;\r
 \r
         int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
                 idWidth);\r
-        int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +\r
-                1) * av.charHeight;\r
+\r
+        int totalHeight = cHeight * (av.alignment.getWidth() / resWidth +1);\r
 \r
         pg.setColor(Color.white);\r
         pg.fillRect(0, 0, pwidth, pheight);\r
         pg.setFont(av.getFont());\r
 \r
+\r
         ////////////////\r
         // Draw the ids\r
         pg.setColor(Color.black);\r
@@ -729,7 +745,7 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
         pg.setClip(0, pi * pheight, pwidth, pheight);\r
 \r
-        int ypos = 2 * av.charHeight;\r
+        int ypos = hgap;\r
 \r
         do\r
         {\r
@@ -748,7 +764,7 @@ public class AlignmentPanel extends GAlignmentPanel
                     (av.charHeight / 5));\r
             }\r
 \r
-            ypos += ((av.alignment.getHeight() + 2) * av.charHeight);\r
+            ypos += cHeight;\r
         }\r
         while (ypos < totalHeight);\r
 \r
@@ -759,8 +775,9 @@ public class AlignmentPanel extends GAlignmentPanel
         if ((pi * pheight) < totalHeight)\r
         {\r
             return Printable.PAGE_EXISTS;\r
+\r
         }\r
-        else\r
+     else\r
         {\r
             return Printable.NO_SUCH_PAGE;\r
         }\r
@@ -824,23 +841,22 @@ public class AlignmentPanel extends GAlignmentPanel
                                         chooser.getSelectedFile().getParent());\r
         }\r
 \r
+\r
         int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
         int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
 \r
+\r
         if (av.getWrapAlignment())\r
         {\r
-          height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
-              av.chunkHeight;\r
+          height = getWrappedHeight();\r
           width = seqPanel.getWidth() + idPanel.getWidth();\r
-\r
         }\r
-\r
-\r
-        if (av.getShowAnnotation())\r
+        else if (av.getShowAnnotation())\r
         {\r
-            height += annotationPanel.getPreferredSize().height;\r
+          height += annotationPanel.adjustPanelHeight()+3;\r
         }\r
 \r
+\r
         try\r
          {\r
            FileOutputStream out = new FileOutputStream(epsFile);\r
@@ -948,6 +964,32 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
     }\r
 \r
+    int getWrappedHeight()\r
+    {\r
+\r
+      int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
+        seqPanel.seqCanvas.getWidth());\r
+\r
+      int hgap = av.charHeight;\r
+      if (av.scaleAboveWrapped)\r
+        hgap += av.charHeight;\r
+\r
+      int annotationHeight = 0;\r
+      if (av.showAnnotation)\r
+      {\r
+        annotationHeight = annotationPanel.adjustPanelHeight();\r
+      }\r
+\r
+      int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+          + hgap\r
+          + annotationHeight;\r
+\r
+\r
+      int height =  ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
+\r
+      return height;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      */\r
@@ -986,16 +1028,12 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
       if (av.getWrapAlignment())\r
       {\r
-        height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
-            av.chunkHeight;\r
+        height = getWrappedHeight();\r
         width = seqPanel.getWidth() + idPanel.getWidth();\r
-\r
       }\r
-\r
-\r
-        if (av.getShowAnnotation())\r
+      else if (av.getShowAnnotation())\r
         {\r
-            height += annotationPanel.getPreferredSize().height;\r
+            height += annotationPanel.adjustPanelHeight()+3;\r
         }\r
 \r
         try\r