JAL-1807 explicit imports (jalview.ws.*)

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 588411e..4c66214 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -29,11 +29,14 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.HTMLOutput;
 import jalview.jbgui.GAlignmentPanel;
 import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -305,7 +308,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public boolean scrollToPosition(SearchResults results)
   {
-    return scrollToPosition(results, true, false);
+    return scrollToPosition(results, 0, true, false);
   }
 
   /**
@@ -318,7 +321,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
   {
-    return scrollToPosition(searchResults, redrawOverview, false);
+    return scrollToPosition(searchResults, 0, redrawOverview, false);
   }
 
   /**
@@ -326,6 +329,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * (if any)
    * 
    * @param results
+   * @param verticalOffset
+   *          if greater than zero, allows scrolling to a position below the
+   *          first displayed sequence
    * @param redrawOverview
    *          - when set, the overview will be recalculated (takes longer)
    * @param centre
@@ -333,6 +339,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return false if results were not found
    */
   public boolean scrollToPosition(SearchResults results,
+          int verticalOffset,
           boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
@@ -391,6 +398,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
           }
         }
       }
+
+      /*
+       * allow for offset of target sequence (actually scroll to one above it)
+       */
+      seqIndex = Math.max(0, seqIndex - verticalOffset);
+
       if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
@@ -521,12 +534,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
       /*
        * Estimate available height in the AlignFrame for alignment +
-       * annotations. Deduct an estimate of 75 for menu bar, scale panel,
+       * annotations. Deduct an estimate for title bar, menu bar, scale panel,
        * hscroll, status bar (as these are not laid out we can't inspect their
-       * actual heights). Insets gives borders including title bar.
+       * actual heights). Insets gives frame borders.
        */
+      int stuff = Platform.isAMac() ? 80 : 100;
       Insets insets = alignFrame.getInsets();
-      int availableHeight = alignFrame.getHeight() - 75 - insets.top
+      int availableHeight = alignFrame.getHeight() - stuff - insets.top
               - insets.bottom;
 
       /*
@@ -1225,7 +1239,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return idwidth.intValue() + 4;
   }
 
-  void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
+  void makeAlignmentImage(ImageMaker.TYPE type, File file)
   {
     long progress = System.currentTimeMillis();
     headless = (System.getProperty("java.awt.headless") != null && System
@@ -1241,14 +1255,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       AlignmentDimension aDimension = getAlignmentDimension();
       try
       {
-        jalview.util.ImageMaker im;
+        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();
@@ -1259,7 +1273,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           imageTitle = alignFrame.getTitle();
         }
 
-        im = new jalview.util.ImageMaker(this, type, imageAction,
+        im = new ImageMaker(this, type, imageAction,
                 aDimension.getWidth(), aDimension.getHeight(), file,
                 imageTitle);
         if (av.getWrapAlignment())
@@ -1345,7 +1359,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void makeEPS(File epsFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
+    makeAlignmentImage(ImageMaker.TYPE.EPS, epsFile);
   }
 
   /**
@@ -1353,12 +1367,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void makePNG(File pngFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
+    makeAlignmentImage(ImageMaker.TYPE.PNG, pngFile);
   }
 
   public void makeSVG(File svgFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
+    makeAlignmentImage(ImageMaker.TYPE.SVG, svgFile);
   }
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
@@ -1378,7 +1392,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
         StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
-        out.println(jalview.io.HTMLOutput.getImageMapHTML());
+        out.println(HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
                 + "\" border=\"0\" usemap=\"#Map\" >"
                 + "<map name=\"Map\">");
@@ -1554,7 +1568,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(this);
     if (av != null)
     {
-      jalview.structure.StructureSelectionManager ssm = av
+      StructureSelectionManager ssm = av
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
@@ -1727,10 +1741,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param sr
    *          holds mapped region(s) of this alignment that we are scrolling
    *          'to'; may be modified for sequence offset by this method
-   * @param seqOffset
+   * @param verticalOffset
    *          the number of visible sequences to show above the mapped region
    */
-  public void scrollToCentre(SearchResults sr, int seqOffset)
+  public void scrollToCentre(SearchResults sr, int verticalOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
@@ -1744,7 +1758,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * This is like AlignmentI.findIndex(seq) but here we are matching the
      * dataset sequence not the aligned sequence
      */
-    int sequenceIndex = 0;
     boolean matched = false;
     for (SequenceI seq : seqs)
     {
@@ -1753,20 +1766,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
         matched = true;
         break;
       }
-      sequenceIndex++;
     }
     if (!matched)
     {
       return; // failsafe, shouldn't happen
     }
-    sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
-    sr.getResults().get(0)
-            .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
 
     /*
      * Scroll to position but centring the target residue.
      */
-    scrollToPosition(sr, true, true);
+    scrollToPosition(sr, verticalOffset, true, true);
   }
 
   /**