X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=190682941a129aca2ff76b5377fa7860c4c803a1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=5bc46f4c998323fc1b589f0994429eff3a496072;hpb=8c6722b27ff92e3610376295e2b4363f942d9969;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 5bc46f4..1906829 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,22 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Container;
@@ -27,6 +43,7 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
+import java.awt.Insets;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.print.PageFormat;
@@ -41,21 +58,6 @@ import java.util.List;
 
 import javax.swing.SwingUtilities;
 
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GAlignmentPanel;
-import jalview.math.AlignmentDimension;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -74,6 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   private IdPanel idPanel;
 
   private boolean headless;
+
   IdwidthAdjuster idwidthAdjuster;
 
   /** DOCUMENT ME!! */
@@ -153,6 +156,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return av;
   }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -175,8 +179,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
             + fm.getDescent()));
     idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
-            .getCharHeight()
-            + fm.getDescent()));
+            .getCharHeight() + fm.getDescent()));
 
     getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
@@ -304,7 +307,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public boolean scrollToPosition(SearchResults results)
   {
-    return scrollToPosition(results, true, false);
+    return scrollToPosition(results, 0, true, false);
   }
 
   /**
@@ -315,9 +318,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+  public boolean scrollToPosition(SearchResults searchResults,
+          boolean redrawOverview)
   {
-    return scrollToPosition(searchResults, redrawOverview, false);
+    return scrollToPosition(searchResults, 0, redrawOverview, false);
   }
 
   /**
@@ -325,6 +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
@@ -332,7 +339,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return false if results were not found
    */
   public boolean scrollToPosition(SearchResults results,
-          boolean redrawOverview, boolean centre)
+          int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
     // TODO: properly locate search results in view when large numbers of hidden
@@ -356,8 +363,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
       // DEBUG
+      // System.err.println(this.av.viewName + " Seq : " + seqIndex
+      // + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -367,7 +375,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
-        end = Math.min(end + offset, seq.getEnd() - 1);
+        end = end + offset - 1;
       }
       if (start < 0)
       {
@@ -390,6 +398,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
           }
         }
       }
+
+      /*
+       * allow for offset of target sequence (actually scroll to one above it)
+       */
+      seqIndex = Math.max(0, seqIndex - verticalOffset);
+
+      // System.out.println("start=" + start + ", end=" + end + ", startv="
+      // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+      // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
@@ -511,47 +528,47 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void validateAnnotationDimensions(boolean adjustPanelHeight)
   {
-    int height = getAnnotationPanel().adjustPanelHeight();
-
-    int theight = av.getCharHeight()
-            * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
-                    : av.getAlignment().getHiddenSequences().getSize()));
-    float sscaling = (float) (theight / (1.0 * theight + height));
-    float ascaling = (float) (height * 1.0 / alignFrame.getHeight());
-    int rheight = alignFrame.getHeight() - height - av.getCharHeight();
+    int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+
     if (adjustPanelHeight)
     {
-      // NOTE: this logic is different in the applet. Need a better algorithm to
-      // define behaviour
-      // try and set height according to alignment
-      if (ascaling > 0 && sscaling < 0.5)
-      {
-        // if the alignment is too big then
-        // default is 0.5 split
-        height = alignFrame.getHeight() / 2;
-      }
-      else
+      int rowHeight = av.getCharHeight();
+      int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+      /*
+       * Estimate available height in the AlignFrame for alignment +
+       * 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 frame borders.
+       */
+      int stuff = Platform.isAMac() ? 80 : 100;
+      Insets insets = alignFrame.getInsets();
+      int availableHeight = alignFrame.getHeight() - stuff - insets.top
+              - insets.bottom;
+
+      /*
+       * If not enough vertical space, maximize annotation height while keeping
+       * at least two rows of alignment visible
+       */
+      if (annotationHeight + alignmentHeight > availableHeight)
       {
-        // if space for more than one sequence row left when annotation is fully
-        // displayed then set height to annotation height
-        // otherwise, leave at least two lines of sequence shown.
-        height = (rheight > av.getCharHeight()) ? height
-                : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling)));
+        annotationHeight = Math.min(annotationHeight, availableHeight - 2
+                * rowHeight);
       }
     }
     else
     {
       // maintain same window layout whilst updating sliders
-      height = annotationScroller.getSize().height;
+      annotationHeight = annotationScroller.getSize().height;
     }
     hscroll.addNotify();
 
     annotationScroller.setPreferredSize(new Dimension(annotationScroller
-            .getWidth(), height));
+            .getWidth(), annotationHeight));
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-            annotationSpaceFillerHolder.getWidth(), height));
-    annotationScroller.validate();// repaint();
+            annotationSpaceFillerHolder.getWidth(), annotationHeight));
+    annotationScroller.validate();
     annotationScroller.addNotify();
   }
 
@@ -656,14 +673,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Adjust row/column scrollers to show a visible position in the alignment.
    * 
    * @param x
-   *          visible column to scroll to DOCUMENT ME!
+   *          visible column to scroll to
    * @param y
    *          visible row to scroll to
    * 
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll to "+x+","+y);
+    // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -731,7 +748,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+              .getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -828,13 +846,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment()
-            .getAlignmentAnnotation(),
+    sorter.sort(getAlignment().getAlignmentAnnotation(),
             av.getSortAnnotationsBy());
     repaint();
 
     if (updateOverview)
     {
+      // TODO: determine if this paintAlignment changed structure colours
       av.getStructureSelectionManager().sequenceColoursChanged(this);
 
       if (overviewPanel != null)
@@ -1046,9 +1064,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 - 4;
       }
 
-      pg.drawString(
-              seq.getDisplayId(av.getShowJVSuffix()),
-              xPos,
+      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
               (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -1057,7 +1073,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
+            endSeq, 0);
 
     if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
     {
@@ -1159,12 +1176,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (labels != null)
       {
-        pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.getCharHeight()));
+        pg.translate(-3,
+                ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.translate(+3, -ypos
+        pg.translate(
+                +3,
+                -ypos
                         - (av.getAlignment().getHeight() * av
                                 .getCharHeight()));
       }
@@ -1174,8 +1193,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
-            0);
+    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+            totalHeight, 0);
 
     if ((pi * pheight) < totalHeight)
     {
@@ -1233,8 +1252,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (alignFrame != null && !headless)
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file", new Object[]
-              { type.getLabel() }), progress);
+              "status.saving_file", new Object[] { type.getLabel() }),
+              progress);
     }
     try
     {
@@ -1295,7 +1314,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       if (alignFrame != null && !headless)
       {
-        alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+        alignFrame.setProgressBar(
+                MessageManager.getString("status.export_complete"),
+                progress);
       }
     }
   }
@@ -1360,6 +1381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
   }
+
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
     // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
@@ -1397,8 +1419,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
             if (av.getAlignment().isNucleotide())
             {
               triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(res)
-                      + "");
+                      .getCharAt(res) + "");
             }
             else
             {
@@ -1420,8 +1441,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\""
                         + (idWidth + res * av.getCharWidth()) + "," + sy
                         + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + ","
-                        + (av.getCharHeight() + sy) + "\""
+                        + "," + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1440,8 +1460,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\""
                         + (idWidth + res * av.getCharWidth()) + "," + sy
                         + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + ","
-                        + (av.getCharHeight() + sy) + "\""
+                        + "," + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1597,10 +1616,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public AlignmentI getAlignment()
   {
-    return av.getAlignment();
+    return av == null ? null : av.getAlignment();
   }
 
-
   @Override
   public String getViewName()
   {
@@ -1652,12 +1670,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     return new FeatureRenderer(this);
   }
-  @Override 
+
+  @Override
   public jalview.api.FeatureRenderer getFeatureRenderer()
   {
     return seqPanel.seqCanvas.getFeatureRenderer();
   }
-  public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+  public void updateFeatureRenderer(
+          jalview.renderer.seqfeatures.FeatureRenderer fr)
   {
     fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
   }
@@ -1727,10 +1748,10 @@ 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 +1765,6 @@ 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 +1773,16 @@ 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);
   }
 
   /**