JAL-3364 tooltip for nucleotide/protein above in exported image

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 3fad3de..4ec71c5 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -36,6 +36,7 @@ import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
@@ -1149,7 +1150,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return idwidth.intValue() + 4;
   }
 
-  void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
+  /**
+   * Generates an image of the alignment panel of the specified type. If
+   * {@code type} is not null, the image is written to the file, otherwise the
+   * user is prompted to specify the output file before writing to it.
+   * 
+   * @param type
+   * @param file
+   * @param forSplitFrame
+   */
+  void makeAlignmentImage(ImageMaker.TYPE type, File file,
+          boolean forSplitFrame)
   {
     int borderBottomOffset = 5;
     long pSessionId = System.currentTimeMillis();
@@ -1166,13 +1177,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     try
     {
-      // todo splitFrame a parameter (optional menu item choice)
-      boolean splitFrame = av.getCodingComplement() != null;
+      /*
+       * if exporting a split frame image, the graphics object has 
+       * width: maximum of the top and bottom image widths
+       * height: sum of the top and bottom image heights
+       */
+      AlignmentPanel comp = null;
       AlignmentDimension dim1 = getAlignmentDimension();
       AlignmentDimension dim2 = new AlignmentDimension(0, 0);
-      if (splitFrame)
+      if (forSplitFrame)
       {
-        AlignmentPanel comp = ((AlignViewport) av.getCodingComplement())
+        comp = ((AlignViewport) av.getCodingComplement())
                 .getAlignPanel();
         dim2 = comp.getAlignmentDimension();
       }
@@ -1180,14 +1195,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
               + borderBottomOffset;
       final int graphicsWidth = Math.max(dim1.width, dim2.width);
 
-      jalview.util.ImageMaker im;
       final String imageAction, imageTitle;
-      if (type == jalview.util.ImageMaker.TYPE.PNG)
+      if (type == ImageMaker.TYPE.PNG)
       {
         imageAction = "Create PNG image from alignment";
         imageTitle = null;
       }
-      else if (type == jalview.util.ImageMaker.TYPE.EPS)
+      else if (type == ImageMaker.TYPE.EPS)
       {
         imageAction = "Create EPS file from alignment";
         imageTitle = alignFrame.getTitle();
@@ -1198,7 +1212,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         imageTitle = alignFrame.getTitle();
       }
 
-      im = new jalview.util.ImageMaker(this, type, imageAction,
+      ImageMaker im = new ImageMaker(this, type, imageAction,
               graphicsWidth, graphicsHeight, file,
               imageTitle, alignFrame, pSessionId, headless);
       Graphics graphics = im.getGraphics();
@@ -1218,15 +1232,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
         printUnwrapped(dim1.width, dim1.height, 0, graphics, graphics);
       }
 
-      if (splitFrame)
+      if (forSplitFrame)
       {
         /*
          * append coding complement image
-         * todo: always write top frame first!
          */
         graphics.translate(0, dim1.height);
-        AlignmentPanel comp = ((AlignViewport) av.getCodingComplement())
-                .getAlignPanel();
         if (av.getCodingComplement().getWrapAlignment())
         {
           comp.printWrappedAlignment(dim2.width,
@@ -1260,8 +1271,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * <li>sequence ids</li>
    * <li>scale above, left or right if shown</li>
    * <li>sequences</li>
-   * <li>annotations, if shown</li> The alignment may be in wrapped or unwrapped
-   * mode.
+   * <li>annotations, if shown</li>
+   * </ul>
+   * The alignment may be in wrapped or unwrapped mode.
    * <ul>
    * 
    * @return
@@ -1302,24 +1314,39 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Creates and writes an EPS image of the alignment, to the given file if
+   * specified, else after prompting for the output file
+   * 
+   * @param epsFile
+   * @param forSplitFrame
    */
-  public void makeEPS(File epsFile)
+  public void makeEPS(File epsFile, boolean forSplitFrame)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
+    makeAlignmentImage(ImageMaker.TYPE.EPS, epsFile, forSplitFrame);
   }
 
   /**
-   * DOCUMENT ME!
+   * Creates and writes a PNG image of the alignment, to the given file if
+   * specified, else after prompting for the output file
+   * 
+   * @param pngFile
+   * @param forSplitFrame
    */
-  public void makePNG(File pngFile)
+  public void makePNG(File pngFile, boolean forSplitFrame)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
+    makeAlignmentImage(ImageMaker.TYPE.PNG, pngFile, forSplitFrame);
   }
 
-  public void makeSVG(File svgFile)
+  /**
+   * Creates and writes an SVG image of the alignment, to the given file if
+   * specified, else after prompting for the output file
+   * 
+   * @param svgFile
+   * @param forSplitFrame
+   */
+  public void makeSVG(File svgFile, boolean forSplitFrame)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
+    makeAlignmentImage(ImageMaker.TYPE.SVG, svgFile, forSplitFrame);
   }
 
   public void makePNGImageMap(File imgMapFile, String imageName)