JAL-629 Fix --headless for new args. Fix progressbar for non-headless commands. Add...

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 5366913..2d057bb 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -123,7 +123,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
-//     setBackground(Color.white);  // BH 2019
+    // setBackground(Color.white); // BH 2019
     alignFrame = af;
     this.av = av;
     setSeqPanel(new SeqPanel(av, this));
@@ -229,6 +229,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // set idCanvas bufferedImage to null
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
+    
+    // update the flag controlling whether the grid is too small to render the font
+    av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
 
     scalePanelHolder.setPreferredSize(
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
@@ -472,8 +475,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
-                + 1);
+        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -573,7 +575,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension e = idPanel.getSize();
     alabels.setSize(new Dimension(e.width, annotationHeight));
 
-
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -1021,8 +1022,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq - 1);
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
+            startRes, endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
@@ -1066,8 +1067,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @throws PrinterException
    */
-  public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
-          Graphics g) throws PrinterException
+  public int printWrappedAlignment(int pageWidth, int pageHeight,
+          int pageNumber, Graphics g) throws PrinterException
   {
     getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
             getHeight());
@@ -1119,8 +1120,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     g.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
-            totalHeight, 0);
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
+            pageWidth - idWidth, totalHeight, 0);
 
     if ((pageNumber * pageHeight) < totalHeight)
     {
@@ -1285,13 +1286,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(column) + "");
+              triplet = ResidueProperties.nucleotideName
+                      .get(seq.getCharAt(column) + "");
             }
             else
             {
-              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
-                      + "");
+              triplet = ResidueProperties.aa2Triplet
+                      .get(seq.getCharAt(column) + "");
             }
 
             if (triplet == null)
@@ -1308,7 +1309,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\"")
                         .append((idWidth + column * av.getCharWidth()))
                         .append(",").append(sy).append(",")
-                        .append((idWidth + (column + 1) * av.getCharWidth()))
+                        .append((idWidth
+                                + (column + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
                         .append(seqPos).append(" ").append(triplet);
@@ -1334,7 +1336,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             }
             if (!Comparison.isGap(seq.getCharAt(column)))
             {
-              List<SequenceFeature> features = seq.findFeatures(column, column);
+              List<SequenceFeature> features = seq.findFeatures(column,
+                      column);
               for (SequenceFeature sf : features)
               {
                 if (sf.isContactFeature())
@@ -1547,11 +1550,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       setAlignFrameView();
     }
   }
+
   public void setAlignFrameView()
   {
     alignFrame.setDisplayedView(this);
   }
-  
+
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
@@ -1741,4 +1745,42 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return calculationDialog;
   }
 
+  /**
+   * Constructs and sets the title for the Overview window (if there is one),
+   * including the align frame's title, and view name (if applicable). Returns
+   * the title, or null if this panel has no Overview window open.
+   * 
+   * @param alignFrame
+   * @return
+   */
+  public String setOverviewTitle(AlignFrame alignFrame)
+  {
+    if (this.overviewPanel == null)
+    {
+      return null;
+    }
+    String overviewTitle = MessageManager
+            .formatMessage("label.overview_params", new Object[]
+            { alignFrame.getTitle() });
+    String viewName = getViewName();
+    if (viewName != null)
+    {
+      overviewTitle += (" " + viewName);
+    }
+    overviewPanel.setTitle(overviewTitle);
+    return overviewTitle;
+  }
+
+  /**
+   * If this alignment panel has an Overview panel open, closes it
+   */
+  public void closeOverviewPanel()
+  {
+    if (overviewPanel != null)
+    {
+      overviewPanel.close();
+      overviewPanel = null;
+    }
+  }
+
 }